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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 A1CF
check button Gene summary
Basic gene informationGene symbolA1CF
Gene nameAPOBEC1 complementation factor
SynonymsACF|ACF64|ACF65|APOBEC1CF|ASP
CytomapUCSC genome browser: 10q11.23
Type of geneprotein-coding
RefGenesNM_001198818.1,
NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,
NM_138933.2,
DescriptionAPOBEC-1 stimulating proteinapo-B RNA editing proteinapobec-1 complementation factor (ACF) (ASP)
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000148584
HPRD : 10627
Vega : OTTHUMG00000018240
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_A1CF
BioGPS: 29974
PathwayNCI Pathway Interaction Database: A1CF
KEGG: A1CF
REACTOME: A1CF
Pathway Commons: A1CF
ContextiHOP: A1CF
ligand binding site mutation search in PubMed: A1CF
UCL Cancer Institute: A1CF
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)LiverStomach
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)LIHCSTAD
Reference showing the relevant tissue of A1CF
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.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0050821protein stabilization12881431
GO:0050821protein stabilization12881431


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TissGeneExp for A1CF

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
COAD5.5493312366.741365851-1.1920346151.37E-056.09E-05
KICH-1.4237992263.339336774-4.7631369.61E-106.02E-09
KIRC5.2370261074.2306330521.0063930560.02140.034084861
KIRP2.3388115244.965136524-2.6263250.0001260.000418507


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TissGene-miRNA for A1CF

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


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TissGeneMut for A1CF
TissGeneSNV for A1CF

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.E34KSKCM5
p.P57SSKCM2
p.Q33*SKCM2
p.L126FSKCM2
p.D329NSKCM2
p.G403ESKCM2
p.G318RSKCM2
p.E50KSKCM2
p.G402ESKCM2
p.G35VHNSC1
p.T37PREAD1
p.R58*SKCM1
p.G10RSKCM1
p.E250DGBM1
p.R587QLUSC1
p.G420RCOAD1
p.G28ESKCM1
p.P426LSKCM1
p.P370SSKCM1
p.K110NUCEC1
p.P6SSKCM1
p.G141WSTAD1
p.A395TSKCM1
p.A565ELGG1
p.E187KBLCA1
p.M85KLUAD1
p.G201ESKCM1
p.G26RSKCM1
p.G208*STAD1
p.K24NSKCM1
p.R392CSKCM1
p.E217QBLCA1
p.Q442*SKCM1
p.A165TPRAD1
p.Y91HCHOL1
p.G407EBLCA1
p.F479LUCEC1
p.E253QLUAD1
p.E270KSKCM1
p.G203DSKCM1
p.A508GLUAD1
p.Y397*HNSC1
p.E120KBLCA1
p.A112GCESC1
p.G28ABLCA1
p.K554EHNSC1
p.S132NPRAD1
p.H360RLIHC1
p.P377SSKCM1
p.R21HHNSC1
p.F587LLUAD1
p.A19VSKCM1
p.R26HOV1
p.E224DSKCM1
p.C9YCOAD1
p.R476THNSC1
p.P345SSKCM1
p.A57VTHYM1
p.G421EHNSC1
p.E154KSKCM1
p.M384ISKCM1
p.G90ELGG1
p.R125HGBM1
p.Q33XSKCM1
p.K9NSKCM1
p.Y76HCHOL1
p.T18ASTAD1
p.A188VLUAD1
p.E77*LUAD1
p.M78KLUAD1
p.E17KSKCM1
p.F68VSTAD1
p.R469THNSC1
p.E508KCOAD1
p.D336NSKCM1
p.P444SLIHC1
p.L119FSKCM1
p.Y404*HNSC1
p.D83NSKCM1
p.A195VLUAD1
p.A188VPAAD1
p.A188VHNSC1
p.E116DLIHC1
p.K89XKIRC1
p.M377ISKCM1
p.R183QPAAD1
p.R259*SKCM1
p.R179*UCEC1
p.G366XLGG1
p.P429HPRAD1
p.N104TLUAD1
p.E71KSKCM1
p.H375RLIHC1
p.S323FSKCM1
p.Y349XTHYM1
p.S125NPRAD1
p.R198QPAAD1
p.S330FSKCM1
p.V184LLUAD1
p.D523NSKCM1
p.D424EBRCA1
p.E57KSKCM1
p.E260QLUAD1
p.A195VPAAD1
p.R47KSKCM1
p.E113KSKCM1
p.A193SLUSC1
p.E64KSKCM1
p.Q333HSKCM1
p.P547LKIRC1
p.T565NGBM1
p.A380VSTAD1
p.A188VPRAD1
p.L31FLIHC1
p.Q485RSTAD1
p.E509KSKCM1
p.E40KSKCM1
p.R364KSKCM1
p.S249PLIHC1
p.G408RPRAD1
p.Q326HSKCM1
p.A203VPRAD1
p.R266XSKCM1
p.V222LOV1
p.A269VUCEC1
p.Q477RSTAD1
p.R580QLUAD1
p.P428SSKCM1
p.R189MLUAD1
p.I254FLUSC1
p.A203VPAAD1
p.G407RPRAD1
p.L233IUCEC1
p.E25KSKCM1
p.K224RPRAD1
p.A396TSKCM1
p.A544TTHYM1
p.A195VBRCA1
p.G7SSKCM1
p.G420ESKCM1
p.F594LLUAD1
p.P436SLUSC1
p.A278TSKCM1
p.G216XSTAD1
p.Q441XSKCM1
p.G149WSTAD1
p.E217DSKCM1
p.V177LLUAD1
p.G11ESKCM1
p.E64*LUAD1
p.E85GLIHC1
p.A285TSKCM1
p.G421ESKCM1
p.E245DCESC1
p.G325RSKCM1
p.E148KHNSC1
p.E120KSKCM1
p.P64SSKCM1
p.P562LKIRC1
p.A349VSTAD1
p.G22SSKCM1
p.P338SSKCM1
p.M149ISKCM1
p.E2KSKCM1
p.G11RSKCM1
p.G336RSKCM1
p.P429TSARC1
p.R373IKIRC1
p.A365VSTAD1
p.P429SSKCM1
p.R307*LGG1


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TissGeneCNV for A1CF

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 A1CF

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
Chimerdb3.0ChiTaRsNABC022263A1CF-ANKDD1Achr10:52623842chr15:65245027
Chimerdb3.0ChiTaRsNAAW300983A1CF-A1CFchr10:52566513chr10:52566487


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TissGeneNet for A1CF

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)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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COAD (tumor)COAD (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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HNSC (tumor)HNSC (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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KICH (tumor)KICH (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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KIRC (tumor)KIRC (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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KIRP (tumor)KIRP (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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LIHC (tumor)LIHC (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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LUAD (tumor)LUAD (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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LUSC (tumor)LUSC (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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PRAD (tumor)PRAD (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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STAD (tumor)STAD (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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THCA (tumor)THCA (normal)
A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (tumor)A1CF, KHSRP, HNF4A, HDAC3, HNF1A, SYNCRIP, APOBEC1, TNPO2, CELF2 (normal)
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TissGeneProg for A1CF

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 A1CF
TissGeneDrug for A1CF

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 A1CF

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0028754Obesity5BeFree
umls:C0009402Colorectal Carcinoma4BeFree
umls:C1527249Colorectal Cancer4BeFree
umls:C0001430Adenoma3BeFree
umls:C0002736Amyotrophic Lateral Sclerosis3BeFree
umls:C0019693HIV Infections3BeFree
umls:C0023452Leukemia, Lymphocytic, Acute, L13BeFree
umls:C3714757Juvenile rheumatoid arthritis3BeFree
umls:C0007131Non-Small Cell Lung Carcinoma2BeFree
umls:C0016037Fibrodysplasia Ossificans Progressiva2BeFree
umls:C0233523Antisocial behavior2BeFree
umls:C0001418Adenocarcinoma1BeFree
umls:C0003873Rheumatoid Arthritis1BeFree
umls:C0008350Cholelithiasis1BeFree
umls:C0011570Mental Depression1BeFree
umls:C0011581Depressive disorder1BeFree
umls:C0011854Diabetes Mellitus, Insulin-Dependent1BeFree
umls:C0023449Acute lymphocytic leukemia1BeFree
umls:C0023493Adult T-Cell Lymphoma/Leukemia1BeFree
umls:C0026946Mycoses1BeFree
umls:C0027627Neoplasm Metastasis1BeFree
umls:C0029408Degenerative polyarthritis1BeFree
umls:C0029925Ovarian Carcinoma1BeFree
umls:C0032584polyps1BeFree
umls:C0036341Schizophrenia1BeFree
umls:C0155877Allergic asthma1BeFree
umls:C0751651Mitochondrial Diseases1BeFree
umls:C0947622Cholecystolithiasis1BeFree
umls:C1140680Malignant neoplasm of ovary1BeFree
umls:C1263846Attention deficit hyperactivity disorder1BeFree
umls:C1535939Pneumocystis jiroveci pneumonia1BeFree
umls:C1956346Coronary Artery Disease1BeFree
umls:C1961102Precursor Cell Lymphoblastic Leukemia Lymphoma1BeFree
umls:C3532239Mitochondrial cardiomyopathy1BeFree