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

Home

Download

Statistics

Help

Contact
Center for Computational Systems Medicine
leaf

Gene summary

leaf

Malignant transformation analysis

leaf

Malignant transformation related pathway analysis

leaf

Cell-cell communication analysis

leaf

Single-cell gene regulatory network inference analysis

leaf

Somatic mutation of malignant transformation related genes

leaf

Related drugs of malignant transformation related genes

Gene: PDS5A

Gene summary for PDS5A

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PDS5A

Gene ID

23244

Gene namePDS5 cohesin associated factor A
Gene AliasPIG54
Cytomap4p14
Gene Typeprotein-coding
GO ID

GO:0000070

UniProtAcc

G1UI16


Top

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
23244PDS5ACCI_1HumanCervixCC3.00e-037.22e-010.528
23244PDS5ACCI_2HumanCervixCC5.54e-099.30e-010.5249
23244PDS5ACCI_3HumanCervixCC7.84e-055.57e-010.516
23244PDS5AHTA11_3410_2000001011HumanColorectumAD9.61e-05-3.07e-010.0155
23244PDS5AHTA11_347_2000001011HumanColorectumAD2.16e-095.74e-01-0.1954
23244PDS5AF007HumanColorectumFAP5.91e-04-2.90e-010.1176
23244PDS5AA001-C-207HumanColorectumFAP8.51e-04-2.44e-010.1278
23244PDS5AA015-C-203HumanColorectumFAP8.23e-37-5.10e-01-0.1294
23244PDS5AA015-C-204HumanColorectumFAP2.29e-09-3.96e-01-0.0228
23244PDS5AA014-C-040HumanColorectumFAP5.45e-07-4.90e-01-0.1184
23244PDS5AA002-C-201HumanColorectumFAP9.92e-17-4.08e-010.0324
23244PDS5AA002-C-203HumanColorectumFAP2.04e-05-2.26e-010.2786
23244PDS5AA001-C-119HumanColorectumFAP9.54e-09-3.79e-01-0.1557
23244PDS5AA001-C-108HumanColorectumFAP2.29e-18-3.05e-01-0.0272
23244PDS5AA002-C-205HumanColorectumFAP4.37e-30-5.26e-01-0.1236
23244PDS5AA001-C-104HumanColorectumFAP3.65e-04-2.04e-010.0184
23244PDS5AA015-C-005HumanColorectumFAP1.57e-06-3.72e-01-0.0336
23244PDS5AA015-C-006HumanColorectumFAP2.03e-21-5.80e-01-0.0994
23244PDS5AA015-C-106HumanColorectumFAP2.96e-12-2.78e-01-0.0511
23244PDS5AA002-C-114HumanColorectumFAP5.17e-25-4.87e-01-0.1561
Page: 1 2 3 4 5 6 7 8 9 10 11 

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
EndometriumThe 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.AEH: Atypical endometrial hyperplasia
EEC: Endometrioid 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
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
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.

Top

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).
Page: 1 2 3 4 5 6 7 8 9 

check button Enriched GO biological processes.
GO IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustCount
GO:00070646CervixCCmitotic sister chromatid cohesion12/231128/187235.47e-058.06e-0412
GO:00062602CervixCCDNA replication48/2311260/187232.70e-031.85e-0248
GO:01400143CervixCCmitotic nuclear division50/2311287/187237.27e-033.91e-0250
GO:00070625CervixCCsister chromatid cohesion15/231162/187237.30e-033.92e-0215
GO:00482851CervixCCorganelle fission78/2311488/187239.70e-034.79e-0278
GO:0007064ColorectumADmitotic sister chromatid cohesion13/391828/187232.22e-031.75e-0213
GO:0007062ColorectumADsister chromatid cohesion23/391862/187232.51e-031.92e-0223
GO:0140014ColorectumADmitotic nuclear division78/3918287/187236.48e-034.05e-0278
GO:00070642ColorectumFAPmitotic sister chromatid cohesion11/262228/187238.55e-048.79e-0311
GO:00070622ColorectumFAPsister chromatid cohesion18/262262/187231.60e-031.42e-0218
GO:00070623ColorectumCRCsister chromatid cohesion16/207862/187239.40e-041.15e-0216
GO:00070643ColorectumCRCmitotic sister chromatid cohesion9/207828/187232.43e-032.30e-029
GO:0006275ColorectumCRCregulation of DNA replication21/2078107/187236.56e-034.70e-0221
GO:00062752EndometriumAEHregulation of DNA replication21/2100107/187237.38e-034.20e-0221
GO:000627511EndometriumEECregulation of DNA replication22/2168107/187235.09e-033.20e-0222
GO:014001414EsophagusESCCmitotic nuclear division218/8552287/187236.17e-261.78e-23218
GO:000007011EsophagusESCCmitotic sister chromatid segregation138/8552168/187231.37e-222.63e-20138
GO:00008194EsophagusESCCsister chromatid segregation157/8552202/187238.41e-211.33e-18157
GO:000705911EsophagusESCCchromosome segregation238/8552346/187231.72e-181.82e-16238
GO:00062604EsophagusESCCDNA replication181/8552260/187233.55e-152.05e-13181
Page: 1 2 3 4 5 6 

check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa041106CervixCCCell cycle36/1267157/84654.94e-031.67e-029.86e-0336
hsa0411013CervixCCCell cycle36/1267157/84654.94e-031.67e-029.86e-0336
hsa04110ColorectumFAPCell cycle37/1404157/84651.44e-024.77e-022.90e-0237
hsa041101ColorectumFAPCell cycle37/1404157/84651.44e-024.77e-022.90e-0237
hsa0411023EsophagusESCCCell cycle126/4205157/84651.34e-155.60e-142.87e-14126
hsa0411033EsophagusESCCCell cycle126/4205157/84651.34e-155.60e-142.87e-14126
hsa041104LiverCirrhoticCell cycle61/2530157/84659.53e-033.21e-021.98e-0261
hsa0411011LiverCirrhoticCell cycle61/2530157/84659.53e-033.21e-021.98e-0261
hsa041102LiverHCCCell cycle106/4020157/84652.54e-073.04e-061.69e-06106
hsa041103LiverHCCCell cycle106/4020157/84652.54e-073.04e-061.69e-06106
hsa041105LungIACCell cycle30/1053157/84651.03e-023.83e-022.54e-0230
hsa0411012LungIACCell cycle30/1053157/84651.03e-023.83e-022.54e-0230
hsa041108Oral cavityOSCCCell cycle118/3704157/84657.15e-162.66e-141.35e-14118
hsa0411015Oral cavityOSCCCell cycle118/3704157/84657.15e-162.66e-141.35e-14118
hsa0411022Oral cavityLPCell cycle70/2418157/84651.17e-058.27e-055.33e-0570
hsa0411032Oral cavityLPCell cycle70/2418157/84651.17e-058.27e-055.33e-0570
hsa0411041Oral cavityEOLPCell cycle42/1218157/84653.20e-051.61e-049.52e-0542
hsa0411051Oral cavityEOLPCell cycle42/1218157/84653.20e-051.61e-049.52e-0542
hsa0411061Oral cavityNEOLPCell cycle37/1112157/84652.29e-041.58e-039.95e-0437
hsa0411071Oral cavityNEOLPCell cycle37/1112157/84652.29e-041.58e-039.95e-0437
Page: 1 2 

Top

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
Page: 1 

Top

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.
Page: 1 

Top

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
PDS5ASNVMissense_Mutationnovelc.1343N>Tp.Asp448Valp.D448VQ29RF7protein_codingdeleterious(0)probably_damaging(0.994)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
PDS5ASNVMissense_Mutationc.1129N>Tp.Arg377Cysp.R377CQ29RF7protein_codingdeleterious(0)probably_damaging(0.999)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
PDS5ASNVMissense_Mutationc.259N>Tp.Arg87Cysp.R87CQ29RF7protein_codingdeleterious(0)probably_damaging(0.997)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
PDS5ASNVMissense_Mutationnovelc.3345N>Ap.Phe1115Leup.F1115LQ29RF7protein_codingtolerated(0.17)possibly_damaging(0.907)TCGA-AX-A2HC-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapypaclitaxelPD
PDS5ASNVMissense_Mutationnovelc.3760G>Tp.Asp1254Tyrp.D1254YQ29RF7protein_codingdeleterious_low_confidence(0.02)benign(0.073)TCGA-AX-A2HD-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnknownUnknownSD
PDS5ASNVMissense_Mutationnovelc.1026A>Cp.Glu342Aspp.E342DQ29RF7protein_codingdeleterious(0.01)probably_damaging(0.997)TCGA-AX-A2HD-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnknownUnknownSD
PDS5ASNVMissense_Mutationc.2910A>Cp.Gln970Hisp.Q970HQ29RF7protein_codingtolerated(0.18)probably_damaging(0.987)TCGA-B5-A11E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
PDS5ASNVMissense_Mutationc.698A>Cp.Lys233Thrp.K233TQ29RF7protein_codingtolerated(0.22)probably_damaging(0.938)TCGA-B5-A11E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
PDS5ASNVMissense_Mutationc.295C>Tp.Arg99Cysp.R99CQ29RF7protein_codingdeleterious(0)probably_damaging(0.998)TCGA-B5-A11U-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnknownUnknownSD
PDS5ASNVMissense_Mutationnovelc.170A>Cp.Gln57Prop.Q57PQ29RF7protein_codingdeleterious(0)probably_damaging(0.998)TCGA-B5-A1MR-01Endometriumuterine corpus endometrioid carcinomaFemale>=65III/IVUnknownUnknownSD
Page: 1 2 3 4 5 6 7 8 9 10 11 12 

Top

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
Page: 1