ToppGene Suite

A one-stop portal for gene list enrichment analysis and candidate gene prioritization
based on functional annotations and protein interactions network

  1. Supplementary File 1: Examples illustrating the utilities of ToppGene Suite

    a. Using ToppFun for gene list enrichment analysis

    b. Using ToppGene for disease gene prioritization based on functional similarity to training set genes

    c. Using ToppNet for disease gene prioritization based on topological features in PPIN

    d. Using ToppGenet to identify and prioritize the neighboring genes of the "seeds" or training set in PPIN

     

  2. Supplementary File 2: List of diseases, training and test set genes used to demonstrate the utility of ToppGene and ToppNet
    1. Results of the 20 candidate gene prioritizations for the below listed five genetic diseases using ToppGene and ToppNet
    2. Bipolar Disorder
    3. Cardiomyopathy
    4. Celiac Disease
    5. Crohn's Disease
    6. Obesity

    References


    Supplementary File 1: Examples illustrating the utilities of ToppGene Suite

    a. Using ToppFun for gene list enrichment analysis

    Query: To conduct gene list enrichment analysis on obesity-associated genes.

    1. From the homepage click on the first link ("ToppFun: Transcriptome, ontology, phenotype, proteome, and pharmacome annotations based gene list functional enrichment analysis")

    2. On the "Gene list enrichment analysis" enter either human gene symbols or human NCBI Entrez Gene IDs in the box against "Training Gene Set" and click on "Submit Query". ToppGene supports RefSeq and UniProt IDs too. For the list of obesity genes, see the Supplementary File 2.

    3. You can select the appropriate statistical parameters under the "Enrichment analysis parameter" and then hit "Submit" button. The default parameters are "Bonferroni" for multiple correction method and 0.05 for significance cut-off level. 4. If your gene list contains non-approved symbols or duplicates at this stage, they will be listed under "Genes Not found". You can then resolve this by selecting the appropriate symbols from a list of suggestions (see 4 below).

    4. If your input gene list contains synonyms or alternate symbols other than approved human gene symbols, you will be prompted to select from a list of alternatives. Once you select the approved symbols, click on the "update" button to allow these genes also to be added back to your input list. This will take back you to the previous screen, wherein after selecting the enrichment analysis parameters you can proceed with the analysis by clicking on "submit" button.

    5. Once the query is processed, the summary "Toppgene Output" screen lists the input parameters and the results. Clicking on the "Show Detail" link opens a pop-up box to see the enriched terms along with p-valuesgene li


    b. Using ToppGene for disease gene prioritization based on functional similarity to training set genes

    Query: To rank or prioritize a list of genes (test set) by functional annotation similarity to training set.

    Here, we will use a list of known obesity associated genes compiled from NCBI's OMIM and Entrez Gene as the training set. The test set is built by creating an artificial linkage interval using a GWAS identified/confirmed obesity genes. In this case, we have used MC4R gene as the candidate gene. The test set is generated by adding 99 nearest neighboring genes of MC4R on the chromosome (99+1=100 test set genes) (see Supplementary File 2 for the lists of training and test set genes) .

    1. From the homepage click on the second link ("ToppGene: Candidate gene prioritization")

    2. On the following page ("Candidate gene prioritization"), enter either gene symbols or Entrez gene IDs, and click "submit query".

    3. Select the appropriate statistical parameters. The "random sampling size" option is for selecting the background gene set from the genome for computing the p-value while the "Min. feature count" represents the number of features that need to be considered for prioritization. The default options are 6% of the genome (or 1500 genes from a total of 25000 genes) for random sampling size and feature count is 2. As described earlier in the enrichment analysis, if your gene lists contain alternate symbols or duplicates they are ignored or presented with the option to resolve them and add them back to your input list. Additionally, if there are common genes between training and test sets (i.e. test set genes which are also found in training set), these will be removed from the test set and no ranks will be assigned to them. After selecting the appropriate statistical parameters (training and test) click on the "start prioritization" button.

    4. Once the analysis is complete, the first half of the results page is similar to what you have seen under enrichment analysis results except that the input parameters show the test set genes also. The prioritized list of test genes sorted according to their ranks based on the p-values are displayed in the lower half. Each column indicates the features used to compute similarity between training and test set.


    c. Using ToppNet for disease gene prioritization based on topological features in protein-protein interactions network (PPIN)

    Query: To rank or prioritize a list of genes (test set) based on topological features in PPIN.

    We will again use the same list of known obesity associated genes compiled from NCBI's OMIM and Entrez Gene as the training set. The test set, as described earlier, is built by creating an artificial linkage interval using a GWAS identified/confirmed obesity genes. In this case, we have used MC4R gene as the candidate gene. The test set is generated by adding 99 nearest neighboring genes of MC4R on the chromosome (99+1=100 test set genes) (see Supplementary File 2 for the lists of training and test set genes). Both the training and test set genes are mapped onto the global PPIN and then the test set genes are scored based on how "close" they are to the training set genes.

    1. From the homepage click on the third link ("ToppNet: relative importance of candidate genes in networks").

    2. On the following page ("Relative importance of candidate genes in protein-protein interaction network"), enter either gene symbols or Entrez gene IDs, and click "submit query".

    3. Select the network prioritization parameters. There are 3 options available (i) K Step Markov (default); (ii) HITS with Priors; and (iii) Page Rank with Priors. Also select the training gene neighborhood subnetwork visualization parameters (default is level 1) and then hit "Start prioritization" button.

    4. Following the prioritization, the test set genes are ranked according to the score. The training gene subnetwork can be exported as a Cytoscape-compatible file. Additionally, the graphical representations of the training gene subnetwork are also presented.


    d. Using ToppGenet to identify and prioritize the neighboring genes of the "seeds" or training set in protein-protein interactions network (PPIN)

    Query: To rank or prioritize a list of genes in the interactome of training set genes using either functional similarity (ToppGene) or PPIN analysis (ToppNet).

    We will continue using the same list of known obesity associated genes compiled from NCBI's OMIM and Entrez Gene as the training set. The test set this time will be composed of genes that are interacting with the training set of genes (level 1 = immediate interactants).

    1. From the homepage click on the fourth option ("ToppGenet: prioritization of neighboring genes in protein-protein interaction network").

    2. Enter the gene symbols and select the options as to how much interactome space you want to be considered, and whether you want to prioritization of the interactome genes to be done by functional similarity (ToppGene) or network analysis (ToppNet). When you select "distance to seeds" as 1, it means that the test set comprises all genes that are immediate interactants of the training set genes. Any overlapping or common genes between the training and test sets will be ignored from the test set and not considered for ranking.

    3. In this example extending the interactome to "level 1" fetches 376 genes which are used as test set after removing the common genes (i.e. those present in the training set too). The final test therefore comprises 33 genes (376-43). The first panel shows the prioritization done through PPIN analysis (ToppNet) while the lower panel shows the prioritization done based on functional similarity (ToppGene).

4. Below is a list of top 25 genes prioritized using ToppNet and ToppGene.


Supplementary File 2: List of diseases, training and test set genes used to demonstrate the utility of ToppGene and ToppNet

The training set of known disease genes were compiled from NCBI's OMIM and Entrez Gene records limiting the search option fields to "Disease/Phenotype" in the latter. The test set genes, as described earlier, were compiled by mixing the GWAS identified/confirmed candidate gene with 99 nearest neighboring genes in the genome (i.e. genes occurring in the flanking regions of the candidate gene).

i. Results of the 20 candidate gene prioritizations for the below listed five genetic diseases using ToppGene and ToppNet.

The gene-disease associations were from recently reported GWAS and include novel disease gene associations. The training sets were compiled using “phenotype/disease” annotations in NCBI’s Entrez Gene records and OMIM. To build the test set genes, we defined the artificial linkage interval to be the set of genes containing the 99 nearest neighboring genes to the novel disease gene based on their genomic distance on the same chromosome. ToppGene and ToppNet prioritization results are presented in below. ToppGene ranked 19/20 (95%) candidate genes within the top 20% while ToppNet ranked 12/16 (75%) candidate genes among the top 20%. The mean ranks for ToppGene and ToppNet based prioritization were 6.8 and 11.75 (excluding 4 disease genes that lacked interaction data) respectively.

Disease Reference Gene ToppGene Rank ToppNet Rank
Bipolar Disorder  Le-Niculescu et al. KLF12 2 15
Bipolar Disorder  Le-Niculescu et al. RORB 4 18
Bipolar Disorder  Le-Niculescu et al. RORA 7 13
Bipolar Disorder  Le-Niculescu et al. ALDH1A1 10 No interaction data
Bipolar Disorder  Le-Niculescu et al. AK3L1 11 No interaction data
Cardiomyopathy Dhandapany et al. MYBPC3 1 2
Celiac Disease Hunt et al. SH2B3 1 8
Celiac Disease Hunt et al. CCR3 2 3
Celiac Disease Hunt et al. IL18R1 3 29
Celiac Disease Hunt et al. RGS1 9 26
Celiac Disease Hunt et al. TAGAP 14 No interaction data
Celiac Disease Hunt et al. IL12A 14 10
Crohns Disease Fisher et al. MST1 1 27
Crohns Disease Fisher et al. NKX2-3 1 27
Crohns Disease Fisher et al. IRGM 2 No interaction data
Crohns Disease Villani et al. NLRP3 5 1
Crohns Disease Fisher et al. IL12B 7 1
Crohns Disease Barrett et al. STAT3 11 1
Franke et al.
Crohns Disease Franke et al. PTPN2 30 6
Obesity Renstrom et al. MC4R 1 1
    Mean 6.8 11.75

ii. Bipolar Disorder

131 Known bipolar disease associated genes (Training set; compiled from OMIM and NCBI Entrez Gene)

Entrez Gene ID Gene Symbol Gene Name
125 ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide
207 AKT1 v-akt murine thymoma viral oncogene homolog 1
79796 ALG9 asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)
288 ANK3 ankyrin 3, node of Ranvier (ankyrin G)
8542 APOL1 apolipoprotein L, 1
23780 APOL2 apolipoprotein L, 2
80832 APOL4 apolipoprotein L, 4
84100 ARL6 ADP-ribosylation factor-like 6
488 ATP2A2 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2
582 BBS1 Bardet-Biedl syndrome 1
79738 BBS10 Bardet-Biedl syndrome 10
166379 BBS12 Bardet-Biedl syndrome 12
583 BBS2 Bardet-Biedl syndrome 2
585 BBS4 Bardet-Biedl syndrome 4
129880 BBS5 Bardet-Biedl syndrome 5
55212 BBS7 Bardet-Biedl syndrome 7
27241 BBS9 Bardet-Biedl syndrome 9
627 BDNF brain-derived neurotrophic factor
56652 C10orf2 chromosome 10 open reading frame 2
400359 C15orf53 chromosome 15 open reading frame 53
778 CACNA1F calcium channel, voltage-dependent, L type, alpha 1F subunit
100133941 CD24 CD24 molecule
80184 CEP290 centrosomal protein 290kDa
1116 CHI3L1 chitinase 3-like 1 (cartilage glycoprotein-39)
4261 CIITA class II, major histocompatibility complex, transactivator
9575 CLOCK clock homolog (mouse)
1243 CMM cutaneous malignant melanoma/dysplastic nevus
474388 CMM4 Melanoma, cutaneous malignant, 4
1312 COMT catechol-O-methyltransferase
1392 CRH corticotropin releasing hormone
1610 DAO D-amino-acid oxidase
267012 DAOA D-amino acid oxidase activator
84516 DCTN5 dynactin 5 (p25)
1714 DGCR DiGeorge syndrome chromosome region
160851 DGKH diacylglycerol kinase, eta
27185 DISC1 disrupted in schizophrenia 1
27184 DISC2 disrupted in schizophrenia 2 (non-protein coding)
1756 DMD dystrophin
1786 DNMT1 DNA (cytosine-5-)-methyltransferase 1
1814 DRD3 dopamine receptor D3
1815 DRD4 dopamine receptor D4
92126 DSEL dermatan sulfate epimerase-like
84062 DTNBP1 dystrobrevin binding protein 1
9030 ERDA1 expanded repeat domain, CAG/CTG 1
2289 FKBP5 FK506 binding protein 5
2332 FMR1 fragile X mental retardation 1
282706 G30 protein LG30-like
2555 GABRA2 gamma-aminobutyric acid (GABA) A receptor, alpha 2
2558 GABRA5 gamma-aminobutyric acid (GABA) A receptor, alpha 5
2629 GBA glucosidase, beta; acid (includes glucosylceramidase)
2774 GNAL guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type
9248 GPR50 G protein-coupled receptor 50
2892 GRIA3 glutamate receptor, ionotrophic, AMPA 3
2913 GRM3 glutamate receptor, metabotropic 3
2932 GSK3B glycogen synthase kinase 3 beta
3119 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1
3123 HLA-DRB1 major histocompatibility complex, class II, DR beta 1
3356 HTR2A 5-hydroxytryptamine (serotonin) receptor 2A
3359 HTR3A 5-hydroxytryptamine (serotonin) receptor 3A
3360 HTR4 5-hydroxytryptamine (serotonin) receptor 4
3575 IL7R interleukin 7 receptor
3612 IMPA1 inositol(myo)-1(or 4)-monophosphatase 1
3613 IMPA2 inositol(myo)-1(or 4)-monophosphatase 2
3782 KCNN3 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3
4095 MAFD1 major affective disorder 1
4096 MAFD2 major affective disorder 2
100188792 MAFD3 Major affective disorder 3, early onset
100126593 MAFD4 Major affective disorder 4
100188843 MAFD5 Major affective disorder 5
100188844 MAFD6 Major affective disorder 6
100196912 MAFD8 Major affective disorder-8, susceptibility to
100196917 MAFD9 Major affective disorder-9, susceptibility to
4128 MAOA monoamine oxidase A
4157 MC1R melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)
431708 MDD1 Major depressive disorder
431709 MDD2 Major depressive disorder 2
10386 MHW1 Mental health wellness 1
50979 MHW2 Mental health wellness 2
8195 MKKS McKusick-Kaufman syndrome
54903 MKS1 Meckel syndrome, type 1
378484 MRX82 mental retardation, X-linked 82
4397 MS multiple sclerosis
4524 MTHFR 5,10-methylenetetrahydrofolate reductase (NADPH)
4618 MYF6 myogenic factor 6 (herculin)
4663 NA neurocanthocytosis
4706 NDUFAB1 NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa
23327 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like
114548 NLRP3 NLR family, pyrin domain containing 3
4842 NOS1 nitric oxide synthase 1 (neuronal)
2908 NR3C1 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
60506 NYX nyctalopin
79728 PALB2 partner and localizer of BRCA2
5116 PCNT pericentrin
5158 PDE6B phosphodiesterase 6B, cGMP-specific, rod, beta
5443 POMC proopiomelanocortin
5573 PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)
5788 PTPRC protein tyrosine phosphatase, receptor type, C
10743 RAI1 retinoic acid induced 1
10125 RASGRP1 RAS guanyl releasing protein 1 (calcium and DAG-regulated)
5649 RELN reelin
5999 RGS4 regulator of G-protein signaling 4
6103 RPGR retinitis pigmentosa GTPase regulator
65078 RTN4R reticulon 4 receptor
63944 SCZD10 schizophrenia disorder 10 (periodic catatonia)
404686 SCZD11 Schizophrenia susceptibility locus, chromosome 10q-related
619488 SCZD12 schizophrenia 12
100196913 SCZD13 Schizophrenia, susceptibility to, 13
6378 SCZD2 schizophrenia disorder 2
6365 SCZD3 schizophrenia disorder 3
8400 SCZD6 schizophrenia disorder 6
8401 SCZD7 schizophrenia disorder 7
8806 SCZD8 schizophrenia disorder 8
6506 SLC1A2 solute carrier family 1 (glial high affinity glutamate transporter), member 2
6507 SLC1A3 solute carrier family 1 (glial high affinity glutamate transporter), member 3
6531 SLC6A3 solute carrier family 6 (neurotransmitter transporter, dopamine), member 3
6532 SLC6A4 solute carrier family 6 (neurotransmitter transporter, serotonin), member 4
6600 SMCR Smith-Magenis syndrome chromosome region
6854 SYN2 synapsin II
8867 SYNJ1 synaptojanin 1
134860 TAAR9 trace amine associated receptor 9
6899 TBX1 T-box 1
6925 TCF4 transcription factor 4
7054 TH tyrosine hydroxylase
91147 TMEM67 transmembrane protein 67
121278 TPH2 tryptophan hydroxylase 2
22954 TRIM32 tripartite motif-containing 32
7226 TRPM2 transient receptor potential cation channel, subfamily M, member 2
123016 TTC8 tetratricopeptide repeat domain 8
6845 VAMP7 vesicle-associated membrane protein 7
7494 XBP1 X-box binding protein 1
7504 XK X-linked Kx blood group (McLeod syndrome)

Bipolar Disorder Test Set genes

KLF12 candidate gene (KLF12 + 99 nearest neighboring genes)

Entrez Gene ID Gene Symbol Gene Name
87769 A2LD1 AIG2-like domain 1
10257 ABCC4 ATP-binding cassette, sub-family C (CFTR/MRP), member 4
440138 ALG11 asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)
540 ATP7B ATPase, Cu++ transporting, beta polypeptide
6315 ATXN8OS ATXN8 opposite strand (non-protein coding)
93081 C13orf27 chromosome 13 open reading frame 27
79866 C13orf34 chromosome 13 open reading frame 34
440145 C13orf37 chromosome 13 open reading frame 37
196541 C13orf39 chromosome 13 open reading frame 39
83446 CCDC70 coiled-coil domain containing 70
26586 CKAP2 cytoskeleton associated protein 2
9071 CLDN10 claudin 10
1203 CLN5 ceroid-lipofuscinosis, neuronal 5
171425 CLYBL citrate lyase beta like
170622 COMMD6 COMM domain containing 6
1602 DACH1 dachshund homolog 1 (Drosophila)
1638 DCT dopachrome tautomerase (dopachrome delta-isomerase, tyrosine-related protein 2)
79758 DHRS12 dehydrogenase/reductase (SDR family) member 12
81624 DIAPH3 diaphanous homolog 3 (Drosophila)
22894 DIS3 DIS3 mitotic control homolog (S. cerevisiae)
5611 DNAJC3 DnaJ (Hsp40) homolog, subfamily C, member 3
23348 DOCK9 dedicator of cytokinesis 9
22873 DZIP1 DAZ interacting protein 1
1910 EDNRB endothelin receptor type B
220108 FAM124A family with sequence similarity 124A
10160 FARP1 FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)
26224 FBXL3 F-box and leucine-rich repeat protein 3
2259 FGF14 fibroblast growth factor 14
100131561 FKSG29 FKSG29
122183 FLJ40296 FLJ40296 protein
2262 GPC5 glypican 5
10082 GPC6 glypican 6
2841 GPR18 G protein-coupled receptor 18
160897 GPR180 G protein-coupled receptor 180
1880 GPR183 G protein-coupled receptor 183
2974 GUCY1B2 guanylate cyclase 1, soluble, beta 2
266722 HS6ST3 heparan sulfate 6-O-sulfotransferase 3
26512 INTS6 integrator complex subunit 6
3843 IPO5 importin 5
9358 ITGBL1 integrin, beta-like 1 (with EGF-like repeat domains)
115207 KCTD12 potassium channel tetramerisation domain containing 12
79070 KDELC1 KDEL (Lys-Asp-Glu-Leu) containing 1
11278 KLF12 Kruppel-like factor 12
688 KLF5 Kruppel-like factor 5 (intestinal)
57626 KLHL1 kelch-like 1 (Drosophila)
11061 LECT1 leukocyte cell derived chemotaxin 1
4008 LMO7 LIM domain 7
79621 RNASEH2B ribonuclease H2, subunit B
220115 LOC220115 TPTE pseudogene
729233 LOC729233 FLJ40296 protein family member
729240 LOC729240 FLJ40296 protein family member
729246 LOC729246 FLJ40296 protein family member
729250 LOC729250 FLJ40296 protein family member
10150 MBNL2 muscleblind-like 2 (Drosophila)
23077 MYCBP2 MYC binding protein 2
259232 NALCN sodium leak channel, non-selective
54602 NDFIP2 Nedd4 family interacting protein 2
4752 NEK3 NIMA (never in mitosis gene a)-related kinase 3
341676 NEK5 NIMA (never in mitosis gene a)-related kinase 5
10562 OLFM4 olfactomedin 4
283491 OR7E156P olfactory receptor, family 7, subfamily E, member 156 pseudogene
27199 OXGR1 oxoglutarate (alpha-ketoglutarate) receptor 1
5095 PCCA propionyl Coenzyme A carboxylase, alpha polypeptide
27253 PCDH17 protocadherin 17
64881 PCDH20 protocadherin 20
5100 PCDH8 protocadherin 8
5101 PCDH9 protocadherin 9
10464 PIBF1 progesterone immunomodulatory binding factor 1
5457 POU4F1 POU class 4 homeobox 1
5911 RAP2A RAP2A, member of RAS oncogene family
64062 RBM26 RNA binding motif protein 26
140432 RNF113B ring finger protein 113B
79596 RNF219 ring finger protein 219
8796 SCEL sciellin
647174 SERPINE3 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3
122060 SLAIN1 SLAIN motif family, member 1
6564 SLC15A1 solute carrier family 15 (oligopeptide transporter), member 1
114798 SLITRK1 SLIT and NTRK-like family, member 1
26050 SLITRK5 SLIT and NTRK-like family, member 5
84189 SLITRK6 SLIT and NTRK-like family, member 6
11166 SOX21 SRY (sex determining region Y)-box 21
10253 SPRY2 sprouty homolog 2 (Drosophila)
8428 STK24 serine/threonine kinase 24 (STE20 homolog, yeast)
10910 SUGT1 SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)
9882 TBC1D4 TBC1 domain family, member 4
81550 TDRD3 tudor domain containing 3
23483 TGDS TDP-glucose 4,6-dehydratase
55901 THSD1 thrombospondin, type I, domain containing 1
374500 THSD1P thrombospondin, type I, domain containing 1 pseudogene
9375 TM9SF2 transmembrane 9 superfamily member 2
84899 TMTC4 transmembrane and tetratricopeptide repeat containing 4
7174 TPP2 tripeptidyl peptidase II
337867 UBAC2 UBA domain containing 2
7347 UCHL3 ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)
55757 UGCGL2 UDP-glucose ceramide glucosyltransferase-like 2
9724 UTP14C UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)
51028 VPS36 vacuolar protein sorting 36 homolog (S. cerevisiae)
115825 WDFY2 WD repeat and FYVE domain containing 2
7546 ZIC2 Zic family member 2 (odd-paired homolog, Drosophila)
85416 ZIC5 Zic family member 5 (odd-paired homolog, Drosophila)

Bipolar Disorder Test Set genes

ALDH1A1 and RORB candidate gene (ALDH1A1 and RORB + 98 nearest neighboring genes)

Entrez Gene ID Gene Symbol Gene Name
23287 AGTPBP1 ATP/GTP binding protein 1
216 ALDH1A1 aldehyde dehydrogenase 1 family, member A1
84210 ANKRD20A1 ankyrin repeat domain 20 family, member A1
441430 ANKRD20A2 ankyrin repeat domain 20 family, member A2
441425 ANKRD20A3 ankyrin repeat domain 20 family, member A3
728747 ANKRD20A4 ankyrin repeat domain 20 family, member A4
301 ANXA1 annexin A1
320 APBA1 amyloid beta (A4) precursor protein-binding, family A, member 1
375719 AQP7P1 aquaporin 7 pseudogene 1
389756 AQP7P2 aquaporin 7 pseudogene 2
441432 AQP7P3 aquaporin 7 pseudogene 3
414328 C9orf103 chromosome 9 open reading frame 103
138255 C9orf135 chromosome 9 open reading frame 135
389766 C9orf153 chromosome 9 open reading frame 153
55071 C9orf40 chromosome 9 open reading frame 40
138199 C9orf41 chromosome 9 open reading frame 41
138240 C9orf57 chromosome 9 open reading frame 57
9413 C9orf61 chromosome 9 open reading frame 61
84267 C9orf64 chromosome 9 open reading frame 64
169693 C9orf71 chromosome 9 open reading frame 71
286234 C9orf79 chromosome 9 open reading frame 79
138241 C9orf85 chromosome 9 open reading frame 85
54981 C9orf95 chromosome 9 open reading frame 95
445571 CBWD3 COBW domain containing 3
220869 CBWD5 COBW domain containing 5
644019 CBWD6 COBW domain containing 6
728788 CCDC29 coiled-coil domain containing 29
23552 CCRK cell cycle related kinase
84131 CEP78 centrosomal protein 78kDa
645345 CHCHD9 coiled-coil-helix-coiled-coil-helix domain containing 9
1514 CTSL1 cathepsin L1
392360 CTSL3 cathepsin L family member 3
1612 DAPK1 death-associated protein kinase 1
51104 FAM108B1 family with sequence similarity 108, member B1
116224 FAM122A family with sequence similarity 122A
548321 FAM27A family with sequence similarity 27, member A
727905 FAM75A5 family with sequence similarity 75, member A5
26165 FAM75A7 family with sequence similarity 75, member A7
404770 FAM75B family with sequence similarity 75, member B
401535 FLJ45537 FLJ45537 protein
389763 FLJ46321 FLJ46321 protein
442425 FOXB2 forkhead box B2
100036519 FOXD4L2 forkhead box D4-like 2
286380 FOXD4L3 forkhead box D4-like 3
349334 FOXD4L4 forkhead box D4-like 4
653427 FOXD4L5 forkhead box D4-like 5
653404 FOXD4L6 forkhead box D4-like 6
257019 FRMD3 FERM domain containing 3
2395 FXN frataxin
2619 GAS1 growth arrest-specific 1
2650 GCNT1 glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)
9615 GDA guanine deaminase
80318 GKAP1 G kinase anchoring protein 1
9630 GNA14 guanine nucleotide binding protein (G protein), alpha 14
2776 GNAQ guanine nucleotide binding protein (G protein), q polypeptide
51280 GOLM1 golgi membrane protein 1
3190 HNRNPK heterogeneous nuclear ribonucleoprotein K
653553 HSPBL2 heat shock 27kDa protein-like 2 pseudogene
81689 ISCA1 iron-sulfur cluster assembly 1 homolog (S. cerevisiae)
387628 KGFLP1 keratinocyte growth factor-like protein 1
654466 KGFLP2 keratinocyte growth factor-like protein 2
55582 KIF27 kinesin family member 27
687 KLF9 Kruppel-like factor 9
100133920 LOC100133920 hypothetical protein LOC100133920
440896 LOC440896 hypothetical gene LOC440896
442421 LOC442421 hypothetical LOC442421
572558 LOC572558 hypothetical locus LOC572558
60560 MAK10 MAK10 homolog, amino-acid N-acetyltransferase subunit (S. cerevisiae)
256691 MAMDC2 MAM domain containing 2
389741 MGC21881 hypothetical locus MGC21881
4915 NTRK2 neurotrophic tyrosine kinase, receptor, type 2
158046 NXNL2 nucleoredoxin-like 2
26578 OSTF1 osteoclast stimulating factor 1
50652 PCA3 prostate cancer antigen 3 (non-protein coding)
5125 PCSK5 proprotein convertase subtilisin/kexin type 5
5239 PGM5 phosphoglucomutase 5
595135 PGM5P2 phosphoglucomutase 5 pseudogene 2
8395 PIP5K1B phosphatidylinositol-4-phosphate 5-kinase, type I, beta
5568 PRKACG protein kinase, cAMP-dependent, catalytic, gamma
158471 PRUNE2 prune homolog 2 (Drosophila)
29968 PSAT1 phosphoserine aminotransferase 1
375743 PTAR1 protein prenyltransferase alpha subunit repeat containing 1
158158 RASEF RAS and EF-hand domain containing
55312 RFK riboflavin kinase
80010 RMI1 RMI1, RecQ mediated genome instability 1, homolog (S. cerevisiae)
6096 RORB RAR-related orphan receptor B
64078 SLC28A3 solute carrier family 28 (sodium-coupled nucleoside transporter), member 3
23137 SMC5 structural maintenance of chromosomes 5
10927 SPIN1 spindlin 1
9414 TJP2 tight junction protein 2 (zona occludens 2)
7088 TLE1 transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)
7091 TLE4 transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)
117531 TMC1 transmembrane channel-like 1
23670 TMEM2 transmembrane protein 2
80036 TRPM3 transient receptor potential cation channel, subfamily M, member 3
140803 TRPM6 transient receptor potential cation channel, subfamily M, member 6
29979 UBQLN1 ubiquilin 1
23230 VPS13A vacuolar protein sorting 13 homolog A (S. cerevisiae)
79670 ZCCHC6 zinc finger, CCHC domain containing 6
7763 ZFAND5 zinc finger, AN1-type domain 5

Bipolar Disorder Test Set genes

RORA candidate gene (RORA + 99 nearest neighboring genes)

Entrez Gene ID Gene Symbol Gene Name
102 ADAM10 ADAM metallopeptidase domain 10
8854 ALDH1A2 aldehyde dehydrogenase 1 family, member A2
348094 ANKDD1A ankyrin repeat and death domain containing 1A
302 ANXA2 annexin A2
83464 APH1B anterior pharynx defective 1 homolog B (C. elegans)
366 AQP9 aquaporin 9
10776 ARPP-19 cyclic AMP phosphoprotein, 19 kD
10017 BCL2L10 BCL2-like 10 (apoptosis facilitator)
663 BNIP2 BCL2/adenovirus E1B 19kDa interacting protein 2
51187 C15orf15 chromosome 15 open reading frame 15
81556 C15orf44 chromosome 15 open reading frame 44
771 CA12 carbonic anhydrase XII
9133 CCNB2 cyclin B2
9236 CCPG1 cell cycle progression 1
84952 CGNL1 cingulin-like 1
8483 CILP cartilage intermediate layer protein, nucleotide pyrophosphohydrolase
10845 CLPX ClpX caseinolytic peptidase X homolog (E. coli)
53944 CSNK1G1 casein kinase 1, gamma 1
23604 DAPK2 death-associated protein kinase 2
10260 DENND4A DENN/MADD domain containing 4A
115752 DIS3L DIS3 mitotic control homolog (S. cerevisiae)-like
54878 DPP8 dipeptidyl-peptidase 8
161582 DYX1C1 dyslexia susceptibility 1 candidate 1
145741 FAM148A family with sequence similarity 148, member A
388125 FAM148B family with sequence similarity 148, member B
54629 FAM63B family with sequence similarity 63, member B
145773 FAM81A family with sequence similarity 81, member A
84191 FAM96A family with sequence similarity 96, member A
283807 FBXL22 F-box and leucine-rich repeat protein 22
27023 FOXB1 forkhead box B1
9245 GCNT3 glucosaminyl (N-acetyl) transferase 3, mucin type
145781 GCOM1 GRINL1A complex locus
10681 GNB5 guanine nucleotide binding protein (G protein), beta 5
81488 GRINL1A glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A
2958 GTF2A2 general transcription factor IIA, 2, 12kDa
390594 hCG_1645727 hCG1645727
8925 HERC1 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1
664618 HSP90AB4P heat shock protein 90kDa alpha (cytosolic), class B member 4 (pseudogene)
9543 IGDCC3 immunoglobulin superfamily, DCC subclass, member 3
57722 IGDCC4 immunoglobulin superfamily, DCC subclass, member 4
9768 KIAA0101 KIAA0101
56204 KIAA1370 KIAA1370
114294 LACTB lactamase, beta
92483 LDHAL6B lactate dehydrogenase A-like 6B
123169 LEO1 Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)
3990 LIPC lipase, hepatic
145783 LOC145783 hypothetical LOC145783
283663 LOC283663 hypothetical LOC283663
5604 MAP2K1 mitogen-activated protein kinase kinase 1
5597 MAPK6 mitogen-activated protein kinase 6
84465 MEGF11 multiple EGF-like-domains 11
55329 MNS1 meiosis-specific nuclear structural 1
123263 MTFMT mitochondrial methionyl-tRNA formyltransferase
4643 MYO1E myosin IE
4644 MYO5A myosin VA (heavy chain 12, myoxin)
55930 MYO5C myosin VC
79664 NARG2 NMDA receptor regulated 2
4734 NEDD4 neural precursor cell expressed, developmentally down-regulated 4
4947 OAZ2 ornithine decarboxylase antizyme 2
3175 ONECUT1 one cut homeobox 1
123264 OSTbeta organic solute transporter beta
54956 PARP16 poly (ADP-ribose) polymerase family, member 16
10081 PDCD7 programmed cell death 7
80119 PIF1 PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)
9488 PIGB phosphatidylinositol glycan anchor biosynthesis, class B
80301 PLEKHO2 pleckstrin homology domain containing, family O member 2
5479 PPIB peptidylprolyl isomerase B (cyclophilin B)
283659 PRTG protogenin homolog (Gallus gallus)
51495 PTPLAD1 protein tyrosine phosphatase-like A domain containing 1
26108 PYGO1 pygopus homolog 1 (Drosophila)
8766 RAB11A RAB11A, member RAS oncogene family
5873 RAB27A RAB27A, member RAS oncogene family
51762 RAB8B RAB8B, member RAS oncogene family
51285 RASL12 RAS-like, family 12
348093 RBPMS2 RNA binding protein with multiple splicing 2
64864 RFX7 regulatory factor X, 7
54778 RNF111 ring finger protein 111
6095 RORA RAR-related orphan receptor A
6124 RPL4 ribosomal protein L4
51065 RPS27L ribosomal protein S27-like
692149 SCARNA14 small Cajal body-specific RNA 14
9187 SLC24A1 solute carrier family 24 (sodium/potassium/calcium exchanger), member 1
79811 SLTM SAFB-like, transcription modulator
10302 SNAPC5 small nuclear RNA activating complex, polypeptide 5, 19kDa
6642 SNX1 sorting nexin 1
79856 SNX22 sorting nexin 22
51324 SPG21 spastic paraplegia 21 (autosomal recessive, Mast syndrome)
6938 TCF12 transcription factor 12
374618 TEX9 testis expressed 9
54962 TIPIN TIMELESS interacting protein
83660 TLN2 talin 2
29766 TMOD3 tropomodulin 3 (ubiquitous)
7168 TPM1 tropomyosin 1 (alpha)
9325 TRIP4 thyroid hormone receptor interactor 4
440279 UNC13C unc-13 homolog C (C. elegans)
9960 USP3 ubiquitin specific peptidase 3
54832 VPS13C vacuolar protein sorting 13 homolog C (S. cerevisiae)
256764 WDR72 WD repeat domain 72
54816 ZNF280D zinc finger protein 280D
23060 ZNF609 zinc finger protein 609

Bipolar Disorder Test Set genes

AK3L1 candidate gene (AK3L1 + 99 nearest neighboring genes)

Entrez Gene ID Gene Symbol Gene Name
34 ACADM acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain
26027 ACOT11 acyl-CoA thioesterase 11
205 AK3L1 adenylate kinase 3-like 1
29929 ALG6 asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)
27329 ANGPTL3 angiopoietin-like 3
81573 ANKRD13C ankyrin repeat domain 13C
84938 ATG4C ATG4 autophagy related 4 homolog C (S. cerevisiae)
7809 BSND Bartter syndrome, infantile, with sensorineural deafness (Barttin)
400757 C1orf141 chromosome 1 open reading frame 141
199920 C1orf168 chromosome 1 open reading frame 168
127254 C1orf173 chromosome 1 open reading frame 173
374977 C1orf175 chromosome 1 open reading frame 175
163747 C1orf177 chromosome 1 open reading frame 177
127428 C1orf83 chromosome 1 open reading frame 83
127795 C1orf87 chromosome 1 open reading frame 87
731 C8A complement component 8, alpha polypeptide
732 C8B complement component 8, beta polypeptide
57685 CACHD1 cache domain containing 1
200008 CDCP2 CUB domain containing protein 2
1429 CRYZ crystallin, zeta (quinone reductase)
1491 CTH cystathionase (cystathionine gamma-lyase)
606495 CYB5RL cytochrome b5 reductase-like
1573 CYP2J2 cytochrome P450, family 2, subfamily J, polypeptide 2
1600 DAB1 disabled homolog 1 (Drosophila)
55635 DEPDC1 DEP domain containing 1
1718 DHCR24 24-dehydrocholesterol reductase
1733 DIO1 deiodinase, iodothyronine, type I
9077 DIRAS3 DIRAS family, GTP-binding RAS-like 3
79469 DLEU2L deleted in lymphocytic leukemia 2-like
9829 DNAJC6 DnaJ (Hsp40) homolog, subfamily C, member 6
85440 DOCK7 dedicator of cytokinesis 7
84455 EFCAB7 EF-hand calcium binding domain 7
338094 FAM151A family with sequence similarity 151, member A
55277 FGGY FGGY carbohydrate kinase domain containing
27022 FOXD3 forkhead box D3
8790 FPGT fucose-1-phosphate guanylyltransferase
1647 GADD45A growth arrest and DNA-damage-inducible, alpha
148979 GLIS1 GLIS family zinc finger 1
55970 GNG12 guanine nucleotide binding protein (G protein), gamma 12
79971 GPR177 G protein-coupled receptor 177
11147 HHLA3 HERV-H LTR-associating 3
51361 HOOK1 hook homolog 1 (Drosophila)
51668 HSPB11 heat shock protein family B (small), member 11
3595 IL12RB2 interleukin 12 receptor, beta 2
149233 IL23R interleukin 23 receptor
10207 INADL InaD-like (Drosophila)
10022 INSL5 insulin-like 5
23421 ITGB3BP integrin beta 3 binding protein (beta3-endonexin)
3716 JAK1 Janus kinase 1 (a protein tyrosine kinase)
3725 JUN jun oncogene
163782 KANK4 KN motif and ankyrin repeat domains 4
54596 L1TD1 LINE-1 type transposase domain containing 1
388633 LDLRAD1 low density lipoprotein receptor class A domain containing 1
3953 LEPR leptin receptor
54741 LEPROT leptin receptor overlapping transcript
431707 LHX8 LIM homeobox 8
55631 LRRC40 leucine rich repeat containing 40
115353 LRRC42 leucine rich repeat containing 42
57554 LRRC7 leucine rich repeat containing 7
127255 LRRIQ3 leucine-rich repeats and IQ motif containing 3
57708 MIER1 mesoderm induction early response 1 homolog (Xenopus laevis)
51253 MRPL37 mitochondrial ribosomal protein L37
114803 MYSM1 myb-like, SWIRM and MPN domains 1
257194 NEGR1 neuronal growth regulator 1
4774 NFIA nuclear factor I/A
115209 OMA1 OMA1 homolog, zinc metallopeptidase (S. cerevisiae)
25973 PARS2 prolyl-tRNA synthetase 2, mitochondrial (putative)
255738 PCSK9 proprotein convertase subtilisin/kexin type 9
5142 PDE4B phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)
55276 PGM2 phosphoglucomutase 2
5301 PIN1L peptidylprolyl cis/trans isomerase, NIMA-interacting 1-like (pseudogene)
8613 PPAP2B phosphatidic acid phosphatase type 2B
5563 PRKAA2 protein kinase, AMP-activated, alpha 2 catalytic subunit
5733 PTGER3 prostaglandin E receptor 3 (subtype EP3)
55225 RAVER2 ribonucleoprotein, PTB-binding 2
4919 ROR1 receptor tyrosine kinase-like orphan receptor 1
6121 RPE65 retinal pigment epithelium-specific protein 65kDa
26135 SERBP1 SERPINE1 mRNA binding protein 1
9295 SFRS11 splicing factor, arginine/serine-rich 11
84251 SGIP1 SH3-domain GRB2-like (endophilin) interacting protein 1
23169 SLC35D1 solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1
204962 SLC44A5 solute carrier family 44, member 5
23648 SSBP3 single stranded DNA binding protein 3
4070 TACSTD2 tumor-associated calcium signal transducer 2
200132 TCTEX1D1 Tctex1 domain containing 1
83941 TM2D1 TM2 domain containing 1
55706 TMEM48 transmembrane protein 48
9528 TMEM59 transmembrane protein 59
199964 TMEM61 transmembrane protein 61
51086 TNNI3K TNNI3 interacting kinase
55001 TTC22 tetratricopeptide repeat domain 22
7268 TTC4 tetratricopeptide repeat domain 4
127253 TYW3 tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)
148581 UBE2U ubiquitin-conjugating enzyme E2U (putative)
7398 USP1 ubiquitin specific peptidase 1
23358 USP24 ubiquitin specific peptidase 24
79819 WDR78 WD repeat domain 78
54432 YIPF1 Yip1 domain family, member 1
9406 ZRANB2 zinc finger, RAN-binding domain containing 2
644928 hCG_2033311 hCG2033311

iii. Cardiomyopathy

98 Known cardiomyopathy associated genes (Training set; compiled from OMIM and NCBI Entrez Gene)

Entrez Gene ID Gene Symbol Gene Name
37 ACADVL acyl-Coenzyme A dehydrogenase, very long chain
58 ACTA1 actin, alpha 1, skeletal muscle
70 ACTC1 actin, alpha, cardiac muscle 1
88 ACTN2 actinin, alpha 2
178 AGL amylo-1, 6-glucosidase, 4-alpha-glucanotransferase
186 AGTR2 angiotensin II receptor, type 2
335 APOA1 apolipoprotein A-I
788 SLC25A20 solute carrier family 25 (carnitine/acylcarnitine translocase), member 20
859 CAV3 caveolin 3
1218 CMD1B cardiomyopathy, dilated 1B (autosomal dominant)
1219 CMD1C cardiomyopathy, dilated 1C (autosomal dominant)
1222 CMD1F cardiomyopathy, dilated 1F (autosomal dominant)
1224 CMD2A cardiomyopathy, dilated 2A (autosomal recessive)
1245 CMR1A cardiomyopathy, restrictive 1A (autosomal dominant)
1246 CMR2A cardiomyopathy, restrictive 2A (autosomal recessive)
1247 CMR3A cardiomyopathy, restrictive 3A (X-linked)
1352 COX10 COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)
1355 COX15 COX15 homolog, cytochrome c oxidase assembly protein (yeast)
1584 CYP11B1 cytochrome P450, family 11, subfamily B, polypeptide 1
1674 DES desmin
1756 DMD dystrophin
1824 DSC2 desmocollin 2
1829 DSG2 desmoglein 2
1832 DSP desmoplakin
2070 EYA4 eyes absent homolog 4 (Drosophila)
2218 FKTN fukutin
2243 FGA fibrinogen alpha chain
2273 FHL1 four and a half LIM domains 1
2395 FXN frataxin
2632 GBE1 glucan (1,4-alpha-), branching enzyme 1
2706 GJB2 gap junction protein, beta 2, 26kDa
2717 GLA galactosidase, alpha
2720 GLB1 galactosidase, beta 1
2934 GSN gelsolin (amyloidosis, Finnish type)
3030 HADHA hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit
3265 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog
3425 IDUA iduronidase, alpha-L-
3728 JUP junction plakoglobin
3845 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
3920 LAMP2 lysosomal-associated membrane protein 2
4000 LMNA lamin A/C
4624 MYH6 myosin, heavy chain 6, cardiac muscle, alpha
4625 MYH7 myosin, heavy chain 7, cardiac muscle, beta
4633 MYL2 myosin, light chain 2, regulatory, cardiac, slow
4634 MYL3 myosin, light chain 3, alkali; ventricular, skeletal, slow
4646 MYO6 myosin VI
4695 NDUFA2 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa
4720 NDUFS2 NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)
4728 NDUFS8 NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase)
4729 NDUFV2 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa
5250 SLC25A3 solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3
5318 PKP2 plakophilin 2
5350 PLN phospholamban
5428 POLG polymerase (DNA directed), gamma
5663 PSEN1 presenilin 1
5664 PSEN2 presenilin 2 (Alzheimer disease 4)
5894 RAF1 v-raf-1 murine leukemia viral oncogene homolog 1
6197 RPS6KA3 ribosomal protein S6 kinase, 90kDa, polypeptide 3
6331 SCN5A sodium channel, voltage-gated, type V, alpha subunit
6443 SGCB sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)
6444 SGCD sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)
6445 SGCG sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)
6584 SLC22A5 solute carrier family 22 (organic cation/carnitine transporter), member 5
6648 SOD2 superoxide dismutase 2, mitochondrial
6654 SOS1 son of sevenless homolog 1 (Drosophila)
6901 TAZ tafazzin
7112 TMPO thymopoietin
7134 TNNC1 troponin C type 1 (slow)
7137 TNNI3 troponin I type 3 (cardiac)
7139 TNNT2 troponin T type 2 (cardiac)
7140 TNNT3 troponin T type 3 (skeletal, fast)
7168 TPM1 tropomyosin 1 (alpha)
7273 TTN titin
7276 TTR transthyretin
7414 VCL vinculin
7840 ALMS1 Alstrom syndrome 1
8048 CSRP3 cysteine and glycine-rich protein 3 (cardiac LIM protein)
8557 TCAP titin-cap (telethonin)
9499 MYOT myotilin
9997 SCO2 SCO cytochrome oxidase deficient homolog 2 (yeast)
10060 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9
10102 TSFM Ts translation elongation factor, mitochondrial
11155 LDB3 LIM domain binding 3
23417 MLYCD malonyl-CoA decarboxylase
23459 CMD1H cardiomyopathy, dilated 1H (autosomal dominant)
26580 BSCL2 Bernardinelli-Seip congenital lipodystrophy 2 (seipin)
29078 C6orf66 chromosome 6 open reading frame 66
51422 PRKAG2 protein kinase, AMP-activated, gamma 2 non-catalytic subunit
56945 MRPS22 mitochondrial ribosomal protein S22
65014 CMD1K cardiomyopathy, dilated 1K (autosomal dominant)
79087 ALG12 asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)
79158 GNPTAB N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits
85366 MYLK2 myosin light chain kinase 2
131118 DNAJC19 DnaJ (Hsp40) homolog, subfamily C, member 19
148738 HFE2 hemochromatosis type 2 (juvenile)
197131 UBR1 ubiquitin protein ligase E3 component n-recognin 1
619468 RCM2 cardiomyopathy, familial restrictive, 2
664728 CMD1Q cardiomyopathy, dilated 1Q (autosomal dominant)

Cardiomyopathy Test Set genes

MYBPC3 candidate gene (MYBPC3 + 99 nearest neighboring genes)

Entrez Gene ID Gene Symbol Gene Name
84680 ACCS 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)
390110 ACCSL 1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like
53 ACP2 acid phosphatase 2, lysosomal
79841 AGBL2 ATP/GTP binding protein-like 2
221120 ALKBH3 alkB, alkylation repair homolog 3 (E. coli)
60529 ALX4 ALX homeobox 4
55626 AMBRA1 autophagy/beclin-1 regulator 1
84364 ARFGAP2 ADP-ribosylation factor GTPase activating protein 2
392 ARHGAP1 Rho GTPase activating protein 1
79096 C11orf49 chromosome 11 open reading frame 49
114900 C1QTNF4 C1q and tumor necrosis factor related protein 4
3732 CD82 CD82 molecule
1132 CHRM4 cholinergic receptor, muscarinic 4
8534 CHST1 carbohydrate (keratan sulfate Gal-6) sulfotransferase 1
9793 CKAP5 cytoskeleton associated protein 5
90993 CREB3L1 cAMP responsive element binding protein 3-like 1
1408 CRY2 cryptochrome 2 (photolyase-like)
10658 CUGBP1 CUG triplet repeat, RNA binding protein 1
1643 DDB2 damage-specific DNA binding protein 2, 48kDa
8525 DGKZ diacylglycerol kinase, zeta 104kDa
2132 EXT2 exostoses (multiple) 2
2147 F2 coagulation factor II (thrombin)
23360 FNBP4 formin binding protein 4
2346 FOLH1 folate hydrolase (prostate-specific membrane antigen) 1
120071 GYLTL1B glycosyltransferase-like 1B
283254 HARBI1 harbinger transposase derived 1
55709 KBTBD4 kelch repeat and BTB (POZ) domain containing 4
9776 KIAA0652 KIAA0652
143678 LOC143678 hypothetical LOC143678
441601 LOC441601 septin 7 pseudogene
646813 LOC646813 hypothetical LOC646813
4038 LRP4 low density lipoprotein receptor-related protein 4
8567 MADD MAP-kinase activating death domain
9479 MAPK8IP1 mitogen-activated protein kinase 8 interacting protein 1
4192 MDK midkine (neurite growth-promoting factor 2)
23788 MTCH2 mitochondrial carrier homolog 2 (C. elegans)
4607 MYBPC3 myosin binding protein C, cardiac
4722 NDUFS3 NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)
10062 NR1H3 nuclear receptor subfamily 1, group H, member 3
23279 NUP160 nucleoporin 160kDa
282770 OR10AG1 olfactory receptor, family 10, subfamily AG, member 1
81328 OR4A15 olfactory receptor, family 4, subfamily A, member 15
81327 OR4A16 olfactory receptor, family 4, subfamily A, member 16
403253 OR4A47 olfactory receptor, family 4, subfamily A, member 47
81318 OR4A5 olfactory receptor, family 4, subfamily A, member 5
119765 OR4B1 olfactory receptor, family 4, subfamily B, member 1
219429 OR4C11 olfactory receptor, family 4, subfamily C, member 11
283093 OR4C12 olfactory receptor, family 4, subfamily C, member 12
283092 OR4C13 olfactory receptor, family 4, subfamily C, member 13
81309 OR4C15 olfactory receptor, family 4, subfamily C, member 15
219428 OR4C16 olfactory receptor, family 4, subfamily C, member 16
256144 OR4C3 olfactory receptor, family 4, subfamily C, member 3
403257 OR4C45 olfactory receptor, family 4, subfamily C, member 45
119749 OR4C46 olfactory receptor, family 4, subfamily C, member 46
219432 OR4C6 olfactory receptor, family 4, subfamily C, member 6
81300 OR4P4 olfactory receptor, family 4, subfamily P, member 4
256148 OR4S1 olfactory receptor, family 4, subfamily S, member 1
219431 OR4S2 olfactory receptor, family 4, subfamily S, member 2
390113 OR4X1 olfactory receptor, family 4, subfamily X, member 1
119764 OR4X2 olfactory receptor, family 4, subfamily X, member 2
219447 OR5AS1 olfactory receptor, family 5, subfamily AS, member 1
390142 OR5D13 olfactory receptor, family 5, subfamily D, member 13
219436 OR5D14 olfactory receptor, family 5, subfamily D, member 14
390144 OR5D16 olfactory receptor, family 5, subfamily D, member 16
219438 OR5D18 olfactory receptor, family 5, subfamily D, member 18
338674 OR5F1 olfactory receptor, family 5, subfamily F, member 1
10798 OR5I1 olfactory receptor, family 5, subfamily I, member 1
282775 OR5J2 olfactory receptor, family 5, subfamily J, member 2
219437 OR5L1 olfactory receptor, family 5, subfamily L, member 1
26338 OR5L2 olfactory receptor, family 5, subfamily L, member 2
390155 OR5T1 olfactory receptor, family 5, subfamily T, member 1
219464 OR5T2 olfactory receptor, family 5, subfamily T, member 2
390154 OR5T3 olfactory receptor, family 5, subfamily T, member 3
390148 OR5W2 olfactory receptor, family 5, subfamily W, member 2
219469 OR8H1 olfactory receptor, family 8, subfamily H, member 1
390151 OR8H2 olfactory receptor, family 8, subfamily H, member 2
390152 OR8H3 olfactory receptor, family 8, subfamily H, member 3
120586 OR8I2 olfactory receptor, family 8, subfamily I, member 2
81168 OR8J3 olfactory receptor, family 8, subfamily J, member 3
390157 OR8K1 olfactory receptor, family 8, subfamily K, member 1
219473 OR8K3 olfactory receptor, family 8, subfamily K, member 3
219453 OR8K5 olfactory receptor, family 8, subfamily K, member 5
29763 PACSIN3 protein kinase C and casein kinase substrate in neurons 3
9409 PEX16 peroxisomal biogenesis factor 16
51317 PHF21A PHD finger protein 21A
56981 PRDM11 PR domain containing 11
5702 PSMC3 proteasome (prosome, macropain) 26S subunit, ATPase, 3
114971 PTPMT1 protein tyrosine phosphatase, mitochondrial 1
5795 PTPRJ protein tyrosine phosphatase, receptor type, J
5913 RAPSN receptor-associated protein of the synapse
55343 SLC35C1 solute carrier family 35, member C1
91252 SLC39A13 solute carrier family 39 (zinc transporter), member 13
692108 SNORD67 small nucleolar RNA, C/D box 67
6688 SPI1 spleen focus forming virus (SFFV) proviral integration oncogene spi1
84767 SPRYD5 SPRY domain containing 5
57586 SYT13 synaptotagmin XIII
9537 TP53I11 tumor protein p53 inducible protein 11
79097 TRIM48 tripartite motif-containing 48
90139 TSPAN18 tetraspanin 18
79797 ZNF408 zinc finger protein 408

iv. Celiac disease

67 Known celiac disease associated genes (Training set; compiled from OMIM and NCBI Entrez Gene)

Entrez Gene ID Gene Symbol Gene Name
100188846 CELIAC6 Celiac disease, susceptibility to, 6
100188870 CELIAC8 Celiac disease, susceptibility to, 8
100188871 CELIAC9 Celiac disease, susceptibility to, 9
100188872 CELIAC10 Celiac disease, susceptibility to, 10
100188873 CELIAC11 Celiac disease, susceptibility to, 11
100188874 CELIAC12 Celiac disease, susceptibility to, 12
100188875 CELIAC13 Celiac disease, susceptibility to, 13
10019 SH2B3 SH2B adaptor protein 3
100233228 IDDM20 Diabetes mellitus, insulin-dependent, 20
100233229 IDDM21 Diabetes mellitus, insulin-dependent, 21
117289 TAGAP T-cell activation RhoGTPase activating protein
1234 CCR5 chemokine (C-C motif) receptor 5
132612 ADAD1 adenosine deaminase domain containing 1 (testis-specific)
1493 CTLA4 cytotoxic T-lymphocyte-associated protein 4
2006 ELN elastin
2022 ENG endoglin
22914 KLRK1 killer cell lectin-like receptor subfamily K, member 1
2591 GALNT3 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)
26191 PTPN22 protein tyrosine phosphatase, non-receptor type 22 (lymphoid)
2677 GGCX gamma-glutamyl carboxylase
2717 GLA galactosidase, alpha
2778 GNAS GNAS complex locus
2969 GTF2I general transcription factor II, i
29970 SCHIP1 schwannomin interacting protein 1
3117 HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1
3119 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1
317782 CELIAC2 celiac disease 2
33 ACADL acyl-Coenzyme A dehydrogenase, long chain
338332 CELIAC5 Celiac disease, susceptibility to, 5
3558 IL2 interleukin 2
3592 IL12A interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)
3600 IL15 interleukin 15
3710 ITPR3 inositol 1,4,5-triphosphate receptor, type 3
3826 KMS Kabuki mental retardation syndrome
389015 SLC9A4 solute carrier family 9 (sodium/hydrogen exchanger), member 4
4026 LPP LIM domain containing preferred translocation partner in lipoma
4276 MICA MHC class I polypeptide-related sequence A
4436 MSH2 mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)
4547 MTTP microsomal triglyceride transfer protein
4650 MYO9B myosin IXB
4763 NF1 neurofibromin 1
4938 OAS1 2',5'-oligoadenylate synthetase 1, 40/46kDa
50854 C6orf48 chromosome 6 open reading frame 48
50943 FOXP3 forkhead box P3
5284 PIGR polymeric immunoglobulin receptor
5621 PRNP prion protein
5651 PRSS7 protease, serine, 7 (enterokinase)
59067 IL21 interleukin 21
5996 RGS1 regulator of G-protein signaling 1
6023 RMRP RNA component of mitochondrial RNA processing endoribonuclease
60498 IGAN IgA nephropathy
6365 SCZD3 schizophrenia disorder 3
6401 SELE selectin E
6402 SELL selectin L
6833 ABCC8 ATP-binding cassette, sub-family C (CFTR/MRP), member 8
6890 TAP1 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)
6927 HNF1A HNF1 homeobox A
7052 TGM2 transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)
7053 TGM3 transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)
791087 HHT4 Telangiectasia, hereditary hemorrhagic, type 4
8074 FGF23 fibroblast growth factor 23
84162 KIAA1109 KIAA1109
8807 IL18RAP interleukin 18 receptor accessory protein
8809 IL18R1 interleukin 18 receptor 1
9173 IL1RL1 interleukin 1 receptor-like 1
9365 KL klotho
9569 GTF2IRD1 GTF2I repeat domain containing 1

Celiac disease Test Set genes for the following six candidate genes is compiled in a similar way as described for others previously.

SH2B3 candidate gene (SH2B3 + 99 nearest neighboring genes)

CCR3 candidate gene (CCR3 + 99 nearest neighboring genes)

IL18R1 candidate gene (IL18R1 + 99 nearest neighboring genes)

RGS1 candidate gene (RGS1 + 99 nearest neighboring genes)

TAGAP candidate gene (TAGAP + 99 nearest neighboring genes)

IL12A candidate gene (IL12A + 99 nearest neighboring genes)

v. Crohn's disease

12 Known Crohn's disease associated genes (Training set; compiled from OMIM and NCBI Entrez Gene)

Entrez Gene ID Gene Symbol Gene Name
183 AGT angiotensinogen (serpin peptidase inhibitor, clade A, member 8)
1673 DEFB4 defensin, beta 4
3569 IL6 interleukin 6 (interferon, beta 2)
3663 IRF5 interferon regulatory factor 5
5243 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1
6583 SLC22A4 solute carrier family 22 (organic cation/ergothioneine transporter), member 4
7466 WFS1 Wolfram syndrome 1 (wolframin)
9231 DLG5 discs, large homolog 5 (Drosophila)
55054 ATG16L1 ATG16 autophagy related 16-like 1 (S. cerevisiae)
64127 NOD2 nucleotide-binding oligomerization domain containing 2
149233 IL23R interleukin 23 receptor
256815 C10orf67 chromosome 10 open reading frame 67

Crohn's disease Test Set genes for the following seven candidate genes is compiled in a similar way as described for others previously.

MST1 candidate gene (MST1 + 99 nearest neighboring genes)

NKX2-3 candidate gene (NKX2-3 + 99 nearest neighboring genes)

IRGM candidate gene (IRGM + 99 nearest neighboring genes)

NLRP3 candidate gene (NLRP3 + 99 nearest neighboring genes)

IL12B candidate gene (IL12B + 99 nearest neighboring genes)

STAT3 candidate gene (STAT3 + 99 nearest neighboring genes)

PTPN2 candidate gene (PTPN2 + 99 nearest neighboring genes)

vi. Obesity

63 Known obesity associated genes (Training set; compiled from OMIM and NCBI Entrez Gene)

Entrez Gene ID Gene Symbol Gene Name
154 ADRB2 adrenergic, beta-2-, receptor, surface
155 ADRB3 adrenergic, beta-3-, receptor
181 AGRP agouti related protein homolog (mouse)
338 APOB apolipoprotein B (including Ag(x) antigen)
627 BDNF brain-derived neurotrophic factor
1270 CNTF ciliary neurotrophic factor
1636 ACE angiotensin I converting enzyme (peptidyl-dipeptidase A) 1
1646 AKR1C2 aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)
1815 DRD4 dopamine receptor D4
2692 GHRHR growth hormone releasing hormone receptor
2784 GNB3 guanine nucleotide binding protein (G protein), beta polypeptide 3
2908 NR3C1 nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
3290 HSD11B1 hydroxysteroid (11-beta) dehydrogenase 1
3557 IL1RN interleukin 1 receptor antagonist
3569 IL6 interleukin 6 (interferon, beta 2)
3643 INSR insulin receptor
3952 LEP leptin
3953 LEPR leptin receptor
3972 LHB luteinizing hormone beta polypeptide
4023 LPL lipoprotein lipase
4159 MC3R melanocortin 3 receptor
4663 NA neurocanthocytosis
4852 NPY neuropeptide Y
4915 NTRK2 neurotrophic tyrosine kinase, receptor, type 2
5122 PCSK1 proprotein convertase subtilisin/kexin type 1
5167 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1
5443 POMC proopiomelanocortin
5465 PPARA peroxisome proliferator-activated receptor alpha
5468 PPARG peroxisome proliferator-activated receptor gamma
5506 PPP1R3A protein phosphatase 1, regulatory (inhibitor) subunit 3A
6197 RPS6KA3 ribosomal protein S6 kinase, 90kDa, polypeptide 3
6303 SAT1 spermidine/spermine N1-acetyltransferase 1
6492 SIM1 single-minded homolog 1 (Drosophila)
6927 HNF1A HNF1 homeobox A
7068 THRB thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)
7350 UCP1 uncoupling protein 1 (mitochondrial, proton carrier)
7351 UCP2 uncoupling protein 2 (mitochondrial, proton carrier)
7352 UCP3 uncoupling protein 3 (mitochondrial, proton carrier)
7492 WTS Wilson-Turner X-linked mental retardation syndrome
8195 MKKS McKusick-Kaufman syndrome
8203 OQTL Obesity quantitative trait locus
8422 MEHMO mental retardation, epileptic seizures, hypogonadism and -genitalism, microcephaly and obesity syndrome
8431 NR0B2 nuclear receptor subfamily 0, group B, member 2
8660 IRS2 insulin receptor substrate 2
9563 H6PD hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)
9607 CARTPT CART prepropeptide
9672 SDC3 syndecan 3
11132 CAPN10 calpain 10
11254 SLC6A14 solute carrier family 6 (amino acid transporter), member 14
23590 PDSS1 prenyl (decaprenyl) diphosphate synthase, subunit 1
50940 PDE11A phosphodiesterase 11A
51738 GHRL ghrelin/obestatin prepropeptide
54903 MKS1 Meckel syndrome, type 1
56694 OB10P obesity, susceptibility to, on chromosome 10p
65076 AOMS1 Abdominal obesity-metabolic syndrome QTL1
65077 AOMS2 abdominal obesity-metabolic syndrome QTL2
80184 CEP290 centrosomal protein 290kDa
116519 APOA5 apolipoprotein A-V
133522 PPARGC1B peroxisome proliferator-activated receptor gamma, coactivator 1 beta
255239 ANKK1 ankyrin repeat and kinase domain containing 1
353126 OB10Q Obesity, susceptibility to, on chromosome 10q
404683 OB4 Obesity, susceptibility to, on chromosome 4
79068 FTO fat mass and obesity associated

Obesity Test Set genes

MC4R candidate gene (MC4R + 99 nearest neighboring genes)

Entrez Gene ID Gene Symbol Gene Name
10449 ACAA2 acetyl-Coenzyme A acyltransferase 2
115701 ALPK2 alpha-kinase 2
5205 ATP8B1 ATPase, class I, type 8B, member 1
374868 ATP9B ATPase, class II, type 9B
596 BCL2 B-cell CLL/lymphoma 2
220134 C18orf24 chromosome 18 open reading frame 24
284254 C18orf26 chromosome 18 open reading frame 26
125704 C18orf51 chromosome 18 open reading frame 51
162681 C18orf54 chromosome 18 open reading frame 54
29090 C18orf55 chromosome 18 open reading frame 55
284274 C18orf62 chromosome 18 open reading frame 62
147381 CBLN2 cerebellin 2 precursor
147372 CCBE1 collagen and calcium binding EGF domains 1
79839 CCDC102B coiled-coil domain containing 102B
220136 CCDC11 coiled-coil domain containing 11
80323 CCDC68 coiled-coil domain containing 68
10666 CD226 CD226 molecule
28513 CDH19 cadherin 19, type 2
28316 CDH20 cadherin 20, type 2
1005 CDH7 cadherin 7, type 2
84735 CNDP1 carnosine dipeptidase 1 (metallopeptidase M20 family)
55748 CNDP2 CNDP dipeptidase 2 (metallopeptidase M20 family)
339302 CPLX4 complexin 4
9150 CTDP1 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1
30827 CXXC1 CXXC finger 1 (PHD domain)
1528 CYB5A cytochrome b5 type A (microsomal)
1630 DCC deleted in colorectal carcinoma
220164 DOK6 docking protein 6
92126 DSEL dermatan sulfate epimerase-like
55520 ELAC1 elaC homolog 1 (E. coli)
201456 FBXO15 F-box protein 15
2235 FECH ferrochelatase (protoporphyria)
2587 GALR1 galanin receptor 1
2922 GRP gastrin-releasing peptide
284293 HMSD histocompatibility (minor) serpin domain containing
2531 KDSR 3-ketodihydrosphingosine reductase
57614 KIAA1468 KIAA1468
9388 LIPG lipase, endothelial
3998 LMAN1 lectin, mannose-binding, 1
284276 LOC284276 hypothetical LOC284276
400657 LOC400657 hypothetical LOC400657
10892 MALT1 mucosa associated lymphoid tissue lymphoma translocation gene 1
5596 MAPK4 mitogen-activated protein kinase 4
4152 MBD1 methyl-CpG binding domain protein 1
8932 MBD2 methyl-CpG binding domain protein 2
4155 MBP myelin basic protein
4160 MC4R melanocortin 4 receptor
4200 ME2 malic enzyme 2, NAD(+)-dependent, mitochondrial
51320 MEX3C mex-3 homolog C (C. elegans)
83876 MRO maestro
4645 MYO5B myosin VB
4677 NARS asparaginyl-tRNA synthetase
23327 NEDD4L neural precursor cell expressed, developmentally down-regulated 4-like
81832 NETO1 neuropilin (NRP) and tolloid (TLL)-like 1
4772 NFATC1 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1
9480 ONECUT2 one cut homeobox 2
23239 PHLPP PH domain and leucine rich repeat protein phosphatase
23556 PIGN phosphatidylinositol glycan anchor biosynthesis, class N
5366 PMAIP1 phorbol-12-myristate-13-acetate-induced protein 1
11201 POLI polymerase (DNA directed) iota
5874 RAB27B RAB27B, member RAS oncogene family
30062 RAX retina and anterior neural fold homeobox
220441 RNF152 ring finger protein 152
25914 RTTN rotatin
27164 SALL3 sal-like 3 (Drosophila)
677769 SCARNA17 small Cajal body-specific RNA 17
90701 SEC11C SEC11 homolog C (S. cerevisiae)
5273 SERPINB10 serpin peptidase inhibitor, clade B (ovalbumin), member 10
89778 SERPINB11 serpin peptidase inhibitor, clade B (ovalbumin), member 11
89777 SERPINB12 serpin peptidase inhibitor, clade B (ovalbumin), member 12
5275 SERPINB13 serpin peptidase inhibitor, clade B (ovalbumin), member 13
5055 SERPINB2 serpin peptidase inhibitor, clade B (ovalbumin), member 2
6317 SERPINB3 serpin peptidase inhibitor, clade B (ovalbumin), member 3
6318 SERPINB4 serpin peptidase inhibitor, clade B (ovalbumin), member 4
5268 SERPINB5 serpin peptidase inhibitor, clade B (ovalbumin), member 5
8710 SERPINB7 serpin peptidase inhibitor, clade B (ovalbumin), member 7
5271 SERPINB8 serpin peptidase inhibitor, clade B (ovalbumin), member 8
4089 SMAD4 SMAD family member 4
677819 SNORA37 small nucleolar RNA, H/ACA box 37
26791 SNORD58A small nucleolar RNA, C/D box 58A
26790 SNORD58B small nucleolar RNA, C/D box 58B
100124516 SNORD58C small nucleolar RNA, C/D box 58C
9306 SOCS6 suppressor of cytokine signaling 6
51046 ST8SIA3 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3
147323 STARD6 StAR-related lipid transfer (START) domain containing 6
6925 TCF4 transcription factor 4
8792 TNFRSF11A tumor necrosis factor receptor superfamily, member 11a, NFKB activator
10194 TSHZ1 teashirt zinc finger homeobox 1
54495 TXNDC10 thioredoxin domain containing 10
9352 TXNL1 thioredoxin-like 1
619491 U58 U58 small nucleolar RNA
9525 VPS4B vacuolar protein sorting 4 homolog B (S. cerevisiae)
23335 WDR7 WD repeat domain 7
284273 ZADH2 zinc binding alcohol dehydrogenase domain containing 2
54877 ZCCHC2 zinc finger, CCHC domain containing 2
7776 ZNF236 zinc finger protein 236
55628 ZNF407 zinc finger protein 407
9658 ZNF516 zinc finger protein 516
55205 ZNF532 zinc finger protein 532
642250 hCG_39912 hCG39912

REFERENCES:

1. Le-Niculescu, H., Patel, S.D., Bhat, M., Kuczenski, R., Faraone, S.V., Tsuang, M.T., McMahon, F.J., Schork, N.J., Nurnberger, J.I., Jr. and Niculescu, A.B., 3rd. (2008) Convergent functional genomics of genome-wide association data for bipolar disorder: Comprehensive identification of candidate genes, pathways and mechanisms. Am J Med Genet B Neuropsychiatr Genet.
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