Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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Center for Computational Systems Medicine
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Gene summary

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Malignant transformation analysis

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Malignant transformation related pathway analysis

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Cell-cell communication analysis

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Single-cell gene regulatory network inference analysis

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Somatic mutation of malignant transformation related genes

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Related drugs of malignant transformation related genes

Gene: FAM13A

Gene summary for FAM13A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

FAM13A

Gene ID

10144

Gene namefamily with sequence similarity 13 member A
Gene AliasARHGAP48
Cytomap4q22.1
Gene Typeprotein-coding
GO ID

GO:0007154

UniProtAcc

O94988


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Malignant transformation analysis

check button Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells
check button Malignant transformation involving gene list.
Entrez IDSymbolReplicatesSpeciesOrganTissueAdj P-valueLog2FCMalignancy
10144FAM13ACCI_1HumanCervixCC1.00e-121.17e+000.528
10144FAM13ACCI_3HumanCervixCC4.66e-065.88e-010.516
10144FAM13AHTA11_3410_2000001011HumanColorectumAD1.25e-09-4.74e-010.0155
10144FAM13AHTA11_696_2000001011HumanColorectumAD2.91e-05-3.59e-01-0.1464
10144FAM13AHTA11_866_3004761011HumanColorectumAD2.60e-03-3.63e-010.096
10144FAM13AHTA11_99999973899_84307HumanColorectumMSS3.23e-02-5.12e-010.2585
10144FAM13AHTA11_99999974143_84620HumanColorectumMSS2.56e-22-6.49e-010.3005
10144FAM13AA015-C-203HumanColorectumFAP9.31e-22-2.28e-01-0.1294
10144FAM13AA015-C-204HumanColorectumFAP9.35e-055.36e-02-0.0228
10144FAM13AA002-C-201HumanColorectumFAP6.51e-12-2.68e-010.0324
10144FAM13AA001-C-119HumanColorectumFAP5.07e-04-1.75e-01-0.1557
10144FAM13AA001-C-108HumanColorectumFAP4.12e-113.77e-02-0.0272
10144FAM13AA002-C-205HumanColorectumFAP5.81e-18-3.16e-01-0.1236
10144FAM13AA015-C-006HumanColorectumFAP4.91e-12-2.62e-01-0.0994
10144FAM13AA015-C-106HumanColorectumFAP1.33e-09-1.58e-01-0.0511
10144FAM13AA002-C-114HumanColorectumFAP1.03e-14-1.93e-01-0.1561
10144FAM13AA015-C-104HumanColorectumFAP8.73e-26-2.78e-01-0.1899
10144FAM13AA001-C-014HumanColorectumFAP1.93e-11-4.71e-020.0135
10144FAM13AA002-C-016HumanColorectumFAP8.19e-18-2.00e-010.0521
10144FAM13AA015-C-002HumanColorectumFAP4.44e-09-1.64e-01-0.0763
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
CervixThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)The image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.FAP: Familial adenomatous polyposis
CRC: Colorectal cancer
Colorectum (HTA11)The image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.AD: Adenomas
SER: Sessile serrated lesions
MSI-H: Microsatellite-high colorectal cancer
MSS: Microsatellite stable colorectal cancer
EsophagusThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.ESCC: Esophageal squamous cell carcinoma
HGIN: High-grade intraepithelial neoplasias
LGIN: Low-grade intraepithelial neoplasias
LiverThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.HCC: Hepatocellular carcinoma
NAFLD: Non-alcoholic fatty liver disease
LungThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.AAH: Atypical adenomatous hyperplasia
AIS: Adenocarcinoma in situ
IAC: Invasive lung adenocarcinoma
MIA: Minimally invasive adenocarcinoma
ProstateThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.BPH: Benign Prostatic Hyperplasia
SkinThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.AK: Actinic keratosis
cSCC: Cutaneous squamous cell carcinoma
SCCIS:squamous cell carcinoma in situ
ThyroidThe image shows the transcriptomic changes along malignancy continuum.log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.ATC: Anaplastic thyroid cancer
HT: Hashimoto's thyroiditis
PTC: Papillary thyroid cancer
∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

check buttonFind out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer
check button Figure of enriched GO biological processes.
TissueDisease StageEnriched GO biological Processes
ColorectumADGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumSERGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumMSSGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumMSI-HGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
ColorectumFAPGO analysis - Figure of enriched GO biological processes: Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).
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check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:00510566CervixCCregulation of small GTPase mediated signal transduction75/2311302/187231.54e-091.74e-0775
GO:0051056ColorectumADregulation of small GTPase mediated signal transduction94/3918302/187231.81e-053.76e-0494
GO:00510561ColorectumMSSregulation of small GTPase mediated signal transduction82/3467302/187231.31e-041.99e-0382
GO:00510562ColorectumFAPregulation of small GTPase mediated signal transduction78/2622302/187233.25e-082.85e-0678
GO:00510563ColorectumCRCregulation of small GTPase mediated signal transduction69/2078302/187233.34e-099.08e-0769
GO:005105610EsophagusESCCregulation of small GTPase mediated signal transduction157/8552302/187231.55e-024.98e-02157
GO:00510564LiverNAFLDregulation of small GTPase mediated signal transduction56/1882302/187234.62e-061.75e-0456
GO:00510565LungIACregulation of small GTPase mediated signal transduction70/2061302/187239.44e-101.87e-0770
GO:005105611LungAISregulation of small GTPase mediated signal transduction66/1849302/187234.26e-109.53e-0866
GO:005105621LungMIACregulation of small GTPase mediated signal transduction35/967302/187236.81e-066.35e-0435
GO:00510568ProstateBPHregulation of small GTPase mediated signal transduction78/3107302/187232.69e-053.16e-0478
GO:005105613ProstateTumorregulation of small GTPase mediated signal transduction80/3246302/187233.96e-054.57e-0480
GO:005105615SkinAKregulation of small GTPase mediated signal transduction48/1910302/187231.28e-039.69e-0348
GO:005105616SkinSCCISregulation of small GTPase mediated signal transduction33/919302/187231.49e-054.86e-0433
GO:005105617ThyroidPTCregulation of small GTPase mediated signal transduction132/5968302/187239.26e-061.04e-04132
GO:005105618ThyroidATCregulation of small GTPase mediated signal transduction141/6293302/187231.43e-061.77e-05141
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
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Cell-cell communication analysis

check buttonIdentification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states
LigandReceptorLRpairPathwayTissueDisease Stage
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Single-cell gene regulatory network inference analysis

check buttonFind out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states
TFCell TypeTissueDisease StageTarget GeneRSSRegulon Activity
∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.
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Somatic mutation of malignant transformation related genes

check buttonAnnotation of somatic variants for genes involved in malignant transformation
Hugo SymbolVariant ClassVariant ClassificationdbSNP RSHGVScHGVSpHGVSp ShortSWISSPROTBIOTYPESIFTPolyPhenTumor Sample BarcodeTissueHistologySexAgeStageTherapy TypesDrugsOutcome
FAM13ASNVMissense_Mutationc.1177N>Cp.Glu393Glnp.E393QO94988protein_codingtolerated(0.4)benign(0.13)TCGA-3C-AALI-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificPoly EComplete Response
FAM13ASNVMissense_Mutationc.1047N>Cp.Leu349Phep.L349FO94988protein_codingdeleterious(0.02)benign(0.383)TCGA-A2-A0EY-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
FAM13ASNVMissense_Mutationc.376N>Ap.Asp126Asnp.D126NO94988protein_codingdeleterious(0.01)benign(0.125)TCGA-A2-A0YK-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
FAM13ASNVMissense_Mutationc.2758G>Ap.Asp920Asnp.D920NO94988protein_codingdeleterious(0)probably_damaging(0.997)TCGA-BH-A0H5-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanCR
FAM13ASNVMissense_Mutationc.1855C>Tp.Arg619Trpp.R619WO94988protein_codingdeleterious(0)probably_damaging(0.999)TCGA-D8-A1XZ-01Breastbreast invasive carcinomaFemale>=65III/IVHormone Therapytamoxiphen+anastrozolumSD
FAM13ASNVMissense_Mutationc.2410G>Cp.Glu804Glnp.E804QO94988protein_codingdeleterious(0)probably_damaging(0.996)TCGA-D8-A27G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
FAM13AinsertionFrame_Shift_Insnovelc.1834_1835insCACTCCCCp.Ser612ThrfsTer38p.S612Tfs*38O94988protein_codingTCGA-A8-A09E-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapyanastrozoleSD
FAM13AinsertionNonsense_Mutationnovelc.2867_2868insTACTTCTTGAAAGTTTGGp.Gln956delinsHisThrSerTerLysPheGlyp.Q956delinsHTS*KFGO94988protein_codingTCGA-AN-A0FX-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
FAM13AinsertionFrame_Shift_Insnovelc.2816_2817insAAp.Leu940SerfsTer20p.L940Sfs*20O94988protein_codingTCGA-AO-A0JM-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
FAM13AinsertionFrame_Shift_Insnovelc.2814_2815insAGAAACTTCGGGATTTTGAAGACAACTTTTTCAGACAGAATp.Gly939ArgfsTer34p.G939Rfs*34O94988protein_codingTCGA-AO-A0JM-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
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Related drugs of malignant transformation related genes

check buttonIdentification of chemicals and drugs interact with genes involved in malignant transfromation
(DGIdb 4.0)
Entrez IDSymbolCategoryInteraction TypesDrug Claim NameDrug NamePMIDs
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