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: XPA

Gene summary for XPA

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

XPA

Gene ID

7507

Gene nameXPA, DNA damage recognition and repair factor
Gene AliasXP1
Cytomap9q22.33
Gene Typeprotein-coding
GO ID

GO:0000715

UniProtAcc

P23025


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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
7507XPALZE2THumanEsophagusESCC8.75e-044.79e-010.082
7507XPALZE4THumanEsophagusESCC3.40e-112.35e-010.0811
7507XPALZE7THumanEsophagusESCC7.67e-074.96e-010.0667
7507XPALZE20THumanEsophagusESCC1.80e-051.89e-010.0662
7507XPALZE22D1HumanEsophagusHGIN7.11e-041.37e-010.0595
7507XPALZE24THumanEsophagusESCC3.38e-123.91e-010.0596
7507XPALZE21THumanEsophagusESCC1.14e-023.46e-010.0655
7507XPAP2T-EHumanEsophagusESCC3.51e-152.96e-010.1177
7507XPAP4T-EHumanEsophagusESCC6.05e-286.54e-010.1323
7507XPAP5T-EHumanEsophagusESCC1.27e-111.70e-010.1327
7507XPAP8T-EHumanEsophagusESCC1.36e-182.75e-010.0889
7507XPAP9T-EHumanEsophagusESCC6.30e-321.01e+000.1131
7507XPAP10T-EHumanEsophagusESCC9.15e-701.38e+000.116
7507XPAP11T-EHumanEsophagusESCC9.50e-165.91e-010.1426
7507XPAP12T-EHumanEsophagusESCC1.39e-317.01e-010.1122
7507XPAP15T-EHumanEsophagusESCC6.94e-317.15e-010.1149
7507XPAP16T-EHumanEsophagusESCC6.74e-172.05e-010.1153
7507XPAP17T-EHumanEsophagusESCC2.41e-043.19e-010.1278
7507XPAP19T-EHumanEsophagusESCC2.62e-073.52e-010.1662
7507XPAP20T-EHumanEsophagusESCC3.78e-152.75e-010.1124
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
Oral CavityThe 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.EOLP: Erosive Oral lichen planus
LP: leukoplakia
NEOLP: Non-erosive oral lichen planus
OSCC: Oral squamous cell carcinoma
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:003450417EsophagusHGINprotein localization to nucleus84/2587290/187231.06e-111.24e-0984
GO:000931418EsophagusHGINresponse to radiation88/2587456/187236.26e-048.65e-0388
GO:00714789EsophagusHGINcellular response to radiation42/2587186/187237.66e-041.00e-0242
GO:00094115EsophagusHGINresponse to UV35/2587149/187239.71e-041.22e-0235
GO:007121418EsophagusHGINcellular response to abiotic stimulus66/2587331/187231.21e-031.45e-0266
GO:010400418EsophagusHGINcellular response to environmental stimulus66/2587331/187231.21e-031.45e-0266
GO:00346445EsophagusHGINcellular response to UV23/258790/187232.16e-032.25e-0223
GO:00094165EsophagusHGINresponse to light stimulus61/2587320/187235.20e-034.30e-0261
GO:00062892EsophagusHGINnucleotide-excision repair16/258760/187236.22e-034.95e-0216
GO:003450418EsophagusESCCprotein localization to nucleus211/8552290/187234.06e-216.60e-19211
GO:000941113EsophagusESCCresponse to UV115/8552149/187233.29e-151.93e-13115
GO:000931419EsophagusESCCresponse to radiation277/8552456/187234.42e-111.43e-09277
GO:003464413EsophagusESCCcellular response to UV70/855290/187234.59e-101.20e-0870
GO:007121419EsophagusESCCcellular response to abiotic stimulus206/8552331/187237.52e-101.88e-08206
GO:010400419EsophagusESCCcellular response to environmental stimulus206/8552331/187237.52e-101.88e-08206
GO:00903053EsophagusESCCnucleic acid phosphodiester bond hydrolysis163/8552261/187233.07e-085.73e-07163
GO:007147816EsophagusESCCcellular response to radiation122/8552186/187233.07e-085.73e-07122
GO:000941611EsophagusESCCresponse to light stimulus183/8552320/187232.03e-051.76e-04183
GO:00062843EsophagusESCCbase-excision repair33/855243/187233.25e-052.69e-0433
GO:00062891EsophagusESCCnucleotide-excision repair42/855260/187231.18e-048.14e-0442
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa034205EsophagusHGINNucleotide excision repair29/138363/84652.96e-085.36e-074.26e-0729
hsa0342012EsophagusHGINNucleotide excision repair29/138363/84652.96e-085.36e-074.26e-0729
hsa0342022EsophagusESCCNucleotide excision repair54/420563/84652.01e-092.17e-081.11e-0854
hsa015247EsophagusESCCPlatinum drug resistance56/420573/84651.85e-061.13e-055.78e-0656
hsa0342032EsophagusESCCNucleotide excision repair54/420563/84652.01e-092.17e-081.11e-0854
hsa0152414EsophagusESCCPlatinum drug resistance56/420573/84651.85e-061.13e-055.78e-0656
hsa015244LiverCirrhoticPlatinum drug resistance34/253073/84651.86e-038.37e-035.16e-0334
hsa03420LiverCirrhoticNucleotide excision repair29/253063/84654.81e-031.74e-021.07e-0229
hsa0152411LiverCirrhoticPlatinum drug resistance34/253073/84651.86e-038.37e-035.16e-0334
hsa034201LiverCirrhoticNucleotide excision repair29/253063/84654.81e-031.74e-021.07e-0229
hsa015242LiverHCCPlatinum drug resistance52/402073/84653.14e-051.88e-041.04e-0452
hsa034202LiverHCCNucleotide excision repair41/402063/84653.59e-031.12e-026.22e-0341
hsa015243LiverHCCPlatinum drug resistance52/402073/84653.14e-051.88e-041.04e-0452
hsa034203LiverHCCNucleotide excision repair41/402063/84653.59e-031.12e-026.22e-0341
hsa034204Oral cavityOSCCNucleotide excision repair49/370463/84653.48e-082.91e-071.48e-0749
hsa015246Oral cavityOSCCPlatinum drug resistance51/370473/84655.41e-062.75e-051.40e-0551
hsa0342011Oral cavityOSCCNucleotide excision repair49/370463/84653.48e-082.91e-071.48e-0749
hsa0152413Oral cavityOSCCPlatinum drug resistance51/370473/84655.41e-062.75e-051.40e-0551
hsa0342021Oral cavityLPNucleotide excision repair37/241863/84655.14e-076.33e-064.08e-0637
hsa0342031Oral cavityLPNucleotide excision repair37/241863/84655.14e-076.33e-064.08e-0637
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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
XPAECMCervixADJTIMP1,FJX1,ZNF737, etc.2.87e-01The 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.
XPAINCAFCervixCCTIMP1,FJX1,ZNF737, etc.3.10e-01The 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.
∗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
XPASNVMissense_Mutationnovelc.765N>Gp.Asp255Glup.D255EP23025protein_codingdeleterious(0.04)benign(0.141)TCGA-MS-A51U-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
XPASNVMissense_Mutationc.569C>Tp.Ser190Phep.S190FP23025protein_codingdeleterious(0)possibly_damaging(0.52)TCGA-JW-A5VL-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
XPAinsertionIn_Frame_Insnovelc.743_744insTAAAACCATAAAAACCCTp.Pro248_Glu249insLysThrIleLysThrLeup.P248_E249insKTIKTLP23025protein_codingTCGA-DS-A1OD-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
XPASNVMissense_Mutationnovelc.637A>Cp.Lys213Glnp.K213QP23025protein_codingtolerated(0.38)benign(0.107)TCGA-CA-6717-01Colorectumcolon adenocarcinomaMale<65I/IIChemotherapyoxaliplatinCR
XPASNVMissense_Mutationc.193N>Ap.Ala65Thrp.A65TP23025protein_codingtolerated(0.78)benign(0)TCGA-G4-6628-01Colorectumcolon adenocarcinomaMale>=65I/IIUnknownUnknownSD
XPASNVMissense_Mutationnovelc.514N>Tp.His172Tyrp.H172YP23025protein_codingtolerated(0.06)benign(0.023)TCGA-A5-A2K5-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
XPASNVMissense_Mutationc.779N>Ap.Thr260Asnp.T260NP23025protein_codingdeleterious(0.03)benign(0.143)TCGA-AJ-A3EK-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIChemotherapycarboplatinCR
XPASNVMissense_Mutationnovelc.566N>Tp.Arg189Metp.R189MP23025protein_codingdeleterious(0)probably_damaging(0.924)TCGA-AP-A05O-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIChemotherapycarboplatinPD
XPASNVMissense_Mutationc.725N>Tp.His242Leup.H242LP23025protein_codingdeleterious(0)probably_damaging(0.997)TCGA-AX-A05S-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnspecificCarboplatin & PaclitaxelPD
XPASNVMissense_Mutationc.484N>Gp.Leu162Valp.L162VP23025protein_codingdeleterious(0.04)benign(0.277)TCGA-AX-A1C8-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnspecificCarboplatinSD
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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
7507XPACLINICALLY ACTIONABLE, DNA REPAIRPlatinum compounds25069034
7507XPACLINICALLY ACTIONABLE, DNA REPAIRIMMUNOSUPPRESSIVE11313422
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