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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for SOX4
check button Gene summary
Basic gene informationGene symbolSOX4
Gene nameSRY (sex determining region Y)-box 4
SynonymsEVI16
CytomapUCSC genome browser: 6p22.3
Type of geneprotein-coding
RefGenesNM_003107.2,
DescriptionSRY-related HMG-box gene 4ecotropic viral integration site 16transcription factor SOX-4
Modification date20141207
dbXrefs MIM : 184430
HGNC : HGNC
Ensembl : ENSG00000124766
HPRD : 01695
Vega : OTTHUMG00000016101
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SOX4
BioGPS: 6659
PathwayNCI Pathway Interaction Database: SOX4
KEGG: SOX4
REACTOME: SOX4
Pathway Commons: SOX4
ContextiHOP: SOX4
ligand binding site mutation search in PubMed: SOX4
UCL Cancer Institute: SOX4
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Bone marrowOvaryThymus
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LAMLOVTHYM
Reference showing the relevant tissue of SOX4
Description by TissGene annotationsProtective TissGene in OS
Cancer gene
TissgsLTS
Fused withOncogene
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0006355regulation of transcription, DNA-templated16631117
GO:0042769DNA damage response, detection of DNA damage19234109
GO:0045893positive regulation of transcription, DNA-templated16631117
GO:0045944positive regulation of transcription from RNA polymerase II promoter19147588
GO:2000761positive regulation of N-terminal peptidyl-lysine acetylation19234109
GO:0006355regulation of transcription, DNA-templated16631117
GO:0042769DNA damage response, detection of DNA damage19234109
GO:0045893positive regulation of transcription, DNA-templated16631117
GO:0045944positive regulation of transcription from RNA polymerase II promoter19147588
GO:2000761positive regulation of N-terminal peptidyl-lysine acetylation19234109


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TissGeneExp for SOX4

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
BLCA1.571331629-0.658099952.2294315791.32E-077.34E-06
LUAD1.280353226-0.3626640151.6430172411.58E-203.58E-19
COAD0.72211503-0.9762811241.6983961541.19E-123.18E-11
PRAD0.506551568-0.558284971.0648365381.02E-102.20E-09
STAD0.669815511-1.1116094891.7814254.81E-131.80E-10
LUSC1.10150779-0.5543059351.6558137252.18E-161.61E-15
THCA0.649035108-0.9346208241.5836559321.18E-141.40E-13


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TissGene-miRNA for SOX4

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples
UCShsa-miR-92b-3pMIMAT00032180.03-0.2956


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TissGeneMut for SOX4
TissGeneSNV for SOX4

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.S149FLIHC1
p.L28VCOAD1
p.F401LLUSC1
p.E111KSKCM1
p.R131MLGG1
p.R110PBLCA1
p.G25CLGG1
p.R131SBLCA1
p.E9DKIRC1
p.G301DSTAD1
p.S459WBLCA1
p.K118ELGG1
p.L100RCOAD1
p.S459WUCS1
p.S418FSKCM1
p.Y449CBLCA1
p.F434CHNSC1
p.P107LGBM1
p.E88KKIRC1
p.A24SKIRP1
p.A112VTHYM1


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TissGeneCNV for SOX4

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for SOX4

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNABU676818SOX4-SOX4chr6:21597211chr6:21597073
Chimerdb3.0ChiTaRsNAAI942449SOX4-SOX4chr6:21595055chr6:21594026
Chimerdb3.0ChiTaRsNAAA909038SOX4-TNNC1chr6:21597212chr3:52486493
Chimerdb3.0ChiTaRsNAAW139952SOX4-GRIP1chr6:21596512chr12:66751619
Chimerdb3.0ChiTaRsNADB315449SOX4-C2CD3chr6:21597192chr11:73753123
Chimerdb3.0ChiTaRsNABF590156SOX4-PSMD14chr6:21595892chr2:162267816
Chimerdb3.0ChiTaRsNAAW207656SOX4-SOX4chr6:21594367chr6:21596527
Chimerdb3.0ChiTaRsNABI088114SOX4-SOX4chr6:21598474chr6:21598430
Chimerdb3.0ChiTaRsNAAI817673SOX4-SOX4chr6:21595876chr6:21594747
Chimerdb3.0ChiTaRsNAAX746958C2CD3-SOX4chr11:73805006chr6:21597111
Chimerdb3.0ChiTaRsNABX478866ATP1A3-SOX4chr19:42470950chr6:21596930


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TissGeneNet for SOX4

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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COAD (tumor)COAD (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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HNSC (tumor)HNSC (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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KICH (tumor)KICH (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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KIRC (tumor)KIRC (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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KIRP (tumor)KIRP (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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LIHC (tumor)LIHC (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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LUAD (tumor)LUAD (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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LUSC (tumor)LUSC (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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PRAD (tumor)PRAD (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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STAD (tumor)STAD (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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THCA (tumor)THCA (normal)
SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (tumor)SOX4, TP53, MDM2, CREBBP, UBE2I, EP300, SDCBP, CD2 (normal)
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TissGeneProg for SOX4

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for SOX4
TissGeneDrug for SOX4

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for SOX4

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0027627Neoplasm Metastasis10BeFree,LHGDN
umls:C0596263Carcinogenesis9BeFree
umls:C0006142Malignant neoplasm of breast6BeFree
umls:C0684249Carcinoma of lung6BeFree
umls:C0242379Malignant neoplasm of lung5BeFree
umls:C0376358Malignant neoplasm of prostate5BeFree
umls:C0001418Adenocarcinoma4BeFree
umls:C0600139Prostate carcinoma4BeFree
umls:C0678222Breast Carcinoma4BeFree
umls:C0007103Malignant neoplasm of endometrium3BeFree
umls:C0007131Non-Small Cell Lung Carcinoma3BeFree
umls:C0023418leukemia3BeFree
umls:C0023467Leukemia, Myelocytic, Acute3BeFree
umls:C0024121Lung Neoplasms3BeFree,LHGDN
umls:C0025149Medulloblastoma3BeFree,LHGDN
umls:C0025202melanoma3BeFree
umls:C0178874Tumor Progression3BeFree
umls:C0476089Endometrial Carcinoma3BeFree
umls:C1883486Uterine Corpus Cancer3BeFree
umls:C2239176Liver carcinoma3BeFree
umls:C0005684Malignant neoplasm of urinary bladder2BeFree
umls:C0005695Bladder Neoplasm2BeFree,LHGDN
umls:C0010606Adenoid Cystic Carcinoma2CTD_human,LHGDN
umls:C0014859Esophageal Neoplasms2BeFree
umls:C0023449Acute lymphocytic leukemia2BeFree
umls:C0023470Myeloid Leukemia2BeFree
umls:C0024623Malignant neoplasm of stomach2BeFree
umls:C0152018Esophageal carcinoma2BeFree
umls:C0278883Metastatic melanoma2BeFree
umls:C0334634Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse2BeFree
umls:C0546837Malignant neoplasm of esophagus2BeFree
umls:C0699791Stomach Carcinoma2BeFree
umls:C0699885Carcinoma of bladder2BeFree
umls:C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma2BeFree
umls:C3539878Triple Negative Breast Neoplasms2BeFree
umls:C0004044Asphyxia1RGD
umls:C0006118Brain Neoplasms1BeFree
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0008479Chondrosarcoma1BeFree
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0009404Colorectal Neoplasms1LHGDN
umls:C0014474Ependymoma1BeFree
umls:C0017636Glioblastoma1BeFree
umls:C0017638Glioma1BeFree
umls:C0018798Congenital Heart Defects1BeFree
umls:C0023493Adult T-Cell Lymphoma/Leukemia1BeFree
umls:C0023904Liver Neoplasms, Experimental1CTD_human
umls:C0029456Osteoporosis1BeFree
umls:C0029463Osteosarcoma1BeFree
umls:C0033578Prostatic Neoplasms1BeFree
umls:C0036095Salivary Gland Neoplasms1CTD_human
umls:C0085110Severe Combined Immunodeficiency1BeFree
umls:C0149782Squamous cell carcinoma of lung1BeFree
umls:C0149925Small cell carcinoma of lung1BeFree
umls:C0151779Cutaneous Melanoma1BeFree
umls:C0175754Agenesis of corpus callosum1BeFree
umls:C0205748Dysplastic Nevus1BeFree
umls:C0206754Neuroendocrine Tumors1BeFree
umls:C0220748Cartilage-hair hypoplasia1BeFree
umls:C0235974Pancreatic carcinoma1BeFree
umls:C0238463Papillary thyroid carcinoma1BeFree
umls:C0278488Carcinoma breast stage IV1BeFree
umls:C0279628Adenocarcinoma Of Esophagus1BeFree
umls:C0346647Malignant neoplasm of pancreas1BeFree
umls:C0585442Osteosarcoma of bone1BeFree
umls:C0598935Tumor Initiation1BeFree
umls:C0699790Colon Carcinoma1BeFree
umls:C0751291Desmoplastic Medulloblastoma1BeFree
umls:C0936248Chondroma1BeFree
umls:C1292769Precursor B-cell lymphoblastic leukemia1BeFree
umls:C1335302Pancreatic Ductal Adenocarcinoma1BeFree
umls:C1458155Mammary Neoplasms1BeFree
umls:C1527249Colorectal Cancer1BeFree