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| TissGeneSummary for VGF |
 Gene summary |
| Basic gene information | Gene symbol | VGF |
| Gene name | VGF nerve growth factor inducible | |
| Synonyms | - | |
| Cytomap | UCSC genome browser: 7q22.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003378.3, | |
| Description | neuro-endocrine specific protein VGFneurosecretory protein VGF | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 602186 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000128564 | ||
| HPRD : 03717 | ||
| Vega : OTTHUMG00000157109 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_VGF | |
| BioGPS: 7425 | ||
| Pathway | NCI Pathway Interaction Database: VGF | |
| KEGG: VGF | ||
| REACTOME: VGF | ||
| Pathway Commons: VGF | ||
| Context | iHOP: VGF | |
| ligand binding site mutation search in PubMed: VGF | ||
| UCL Cancer Institute: VGF | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | HPA,TiGER | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | BrainPancreasSkin | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | GBM,LGGPAADSKCM | |
| Reference showing the relevant tissue of VGF | ||
| Description by TissGene annotations | ||
| * 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. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID |
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| TissGeneExp for VGF |
| 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) |
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| 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) |
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| 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. |
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| 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) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| LUSC | -1.085639469 | -3.134043391 | 2.048403922 | 2.28E-10 | 8.29E-10 |
| LUAD | -0.697463641 | -2.620687779 | 1.923224138 | 9.27E-09 | 4.20E-08 |
| HNSC | -0.715645397 | -2.279126792 | 1.563481395 | 4.67E-07 | 3.89E-06 |
| BRCA | -1.335918571 | -3.107852782 | 1.771934211 | 4.35E-17 | 2.57E-16 |
| KIRP | 0.693542394 | -1.059120106 | 1.7526625 | 0.012 | 0.025819578 |
| COAD | 1.263890471 | 0.049336624 | 1.214553846 | 0.00149 | 0.004106403 |
| THCA | -0.851467352 | -2.231206335 | 1.379738983 | 0.00121 | 0.002778983 |
| PRAD | -0.247409529 | -1.252371068 | 1.004961538 | 0.000157 | 0.000636233 |
| KICH | -2.426082606 | -0.491702606 | -1.93438 | 0.000212 | 0.000520901 |
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| TissGene-miRNA for VGF |
| 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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for VGF |
| TissGeneSNV for VGF |
| 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. |
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| 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) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.E433K | BLCA | 2 |
| p.D443E | STAD | 2 |
| p.E416D | STAD | 1 |
| p.K267N | UCEC | 1 |
| p.Q270* | HNSC | 1 |
| p.S229Y | LUAD | 1 |
| p.E384G | ESCA | 1 |
| p.E591K | BLCA | 1 |
| p.R584P | HNSC | 1 |
| p.L223R | LUSC | 1 |
| p.Q75K | LUAD | 1 |
| p.S150N | LUAD | 1 |
| p.E604D | CESC | 1 |
| p.L197M | COAD | 1 |
| p.P498S | SKCM | 1 |
| p.Q103K | LUAD | 1 |
| p.E144* | LUAD | 1 |
| p.E260K | LUSC | 1 |
| p.E477V | KIRP | 1 |
| p.E179Q | PRAD | 1 |
| p.A174T | STAD | 1 |
| p.P200S | LGG | 1 |
| p.S131R | ACC | 1 |
| p.S559L | BLCA | 1 |
| p.E433Q | BLCA | 1 |
| p.Q103* | CESC | 1 |
| p.R80Q | BLCA | 1 |
| p.R419C | LIHC | 1 |
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| TissGeneCNV for VGF |
| 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) |
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| TissGeneFusions for VGF |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
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| TissGeneNet for VGF |
| 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) |
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| TissGeneProg for VGF |
| 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. |
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| 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. |
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| 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. |
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| 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. |
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| TissGeneClin for VGF |
| TissGeneDrug for VGF |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for VGF |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0002736 | Amyotrophic Lateral Sclerosis | 3 | BeFree,LHGDN |
| umls:C0004936 | Mental disorders | 3 | BeFree |
| umls:C0005586 | Bipolar Disorder | 2 | BeFree |
| umls:C0006142 | Malignant neoplasm of breast | 2 | BeFree |
| umls:C0011570 | Mental Depression | 2 | BeFree |
| umls:C0011581 | Depressive disorder | 2 | BeFree |
| umls:C0678222 | Breast Carcinoma | 2 | BeFree |
| umls:C0002395 | Alzheimer's Disease | 1 | GAD |
| umls:C0004352 | Autistic Disorder | 1 | GAD |
| umls:C0005684 | Malignant neoplasm of urinary bladder | 1 | BeFree |
| umls:C0011847 | Diabetes | 1 | BeFree |
| umls:C0011849 | Diabetes Mellitus | 1 | BeFree |
| umls:C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 1 | BeFree |
| umls:C0020507 | Hyperplasia | 1 | LHGDN |
| umls:C0025268 | Multiple Endocrine Neoplasia Type 2a | 1 | BeFree |
| umls:C0028754 | Obesity | 1 | BeFree |
| umls:C0029925 | Ovarian Carcinoma | 1 | BeFree |
| umls:C0031511 | Pheochromocytoma | 1 | BeFree |
| umls:C0032002 | Pituitary Diseases | 1 | BeFree |
| umls:C0036220 | Kaposi Sarcoma | 1 | BeFree |
| umls:C0038358 | Gastric ulcer | 1 | CTD_human |
| umls:C0041696 | Unipolar Depression | 1 | BeFree |
| umls:C0151786 | Muscle Weakness | 1 | LHGDN |
| umls:C0338831 | Manic | 1 | BeFree |
| umls:C0525045 | Mood Disorders | 1 | BeFree |
| umls:C0677886 | Epithelial ovarian cancer | 1 | BeFree |
| umls:C0699885 | Carcinoma of bladder | 1 | BeFree |
| umls:C1140680 | Malignant neoplasm of ovary | 1 | BeFree |
| umls:C1168401 | Squamous cell carcinoma of the head and neck | 1 | BeFree |
| umls:C1269683 | Major Depressive Disorder | 1 | BeFree |
| umls:C3178803 | Social Anhedonia | 1 | BeFree |
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