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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PIGF |
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Phenotypic Information for PIGF(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PIGF |
Familial Cancer Database: PIGF |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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REACTOME_METABOLISM_OF_PROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PIGF |
MedGen: PIGF (Human Medical Genetics with Condition) | |
ClinVar: PIGF | |
Phenotype | MGI: PIGF (International Mouse Phenotyping Consortium) |
PhenomicDB: PIGF |
Mutations for PIGF |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | PIGF | chr2 | 46839166 | 46839186 | chr2 | 46995260 | 46995280 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PIGF related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BC039303 | PIGF | 1 | 3453 | 2 | 46839366 | 46844169 | C14orf159 | 3452 | 4401 | 14 | 91691027 | 91691976 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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Stat. for Non-Synonymous SNVs (# total SNVs=10) | (# total SNVs=2) |
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(# total SNVs=0) | (# total SNVs=0) |
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* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr2:46808672-46808672 | p.I202T | 2 |
chr2:46839477-46839477 | p.A109A | 2 |
chr2:46840918-46840918 | p.G79R | 1 |
chr2:46808622-46808622 | p.N219H | 1 |
chr2:46842079-46842079 | p.H75H | 1 |
chr2:46808671-46808671 | p.I202I | 1 |
chr2:46842099-46842099 | p.K69E | 1 |
chr2:46842119-46842119 | p.V62A | 1 |
chr2:46808676-46808676 | p.V201F | 1 |
chr2:46842192-46842192 | p.E38Q | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 |   |   | 1 | 1 |   |   |   |   |   |   |   | 1 |   |   |   | 2 | 1 |   | 3 |
# mutation | 2 |   |   | 1 | 1 |   |   |   |   |   |   |   | 1 |   |   |   | 2 | 1 |   | 3 |
nonsynonymous SNV | 2 |   |   | 1 | 1 |   |   |   |   |   |   |   | 1 |   |   |   | 2 | 1 |   | 2 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr2:46842248 | p.I202M | 1 |
chr2:46808671 | p.I202T | 1 |
chr2:46808672 | p.E107Q,PIGF | 1 |
chr2:46840834 | p.L88R,PIGF | 1 |
chr2:46840890 | p.L81S,PIGF | 1 |
chr2:46840911 | p.G79R,PIGF | 1 |
chr2:46840918 | p.H75H,PIGF | 1 |
chr2:46842079 | p.K69E,PIGF | 1 |
chr2:46842099 | p.E38Q,PIGF | 1 |
chr2:46842192 | p.E32D,PIGF | 1 |
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* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
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cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for PIGF |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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BOLA3,ATRAID,CISD2,COX7A2,COX7A2L,CRIPT,DAD1, DYNC2LI1,IAH1,MCTS1,MDH1,MRPL33,MRPL35,NFU1, NUDCD2,PIGF,PSMA2,RAB1A,RDH14,RPA3,UNC50 | ACTR10,ANAPC13,ATP8B5P,C18orf32,COMMD8,DAD1,DERA, GNG5,GTF2A2,IER3IP1,MGST2,MRPS18C,NOP10,PIGF, POMP,RPS27L,SELT,SUMO1,TMEM126B,TOMM5,TSEN15 |
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ACP1,ATP5C1,ATP5F1,ATP5G3,TEFM,CALM2,CKS2, CNIH1,COX7A2L,DPY30,FAM96A,GEMIN6,MCEE,MDH1, MEMO1,MRPL33,MRPL35,NFU1,OST4,PIGF,SNRPG | ARFIP1,ATP5F1,CHCHD1,COX16,DCTPP1,FAM96A,FPGT, MRPL13,MRPS33,MRPS35,NUDT15,NXT2,PEX7,PIGF, PPA2,RFWD2,SFT2D1,TMED5,TMEM68,TXNDC12,UQCRH |
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* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Pharmacological Information for PIGF |
There's no related Drug. |
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Cross referenced IDs for PIGF |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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