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: PTBP1

Gene summary for PTBP1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PTBP1

Gene ID

5725

Gene namepolypyrimidine tract binding protein 1
Gene AliasHNRNP-I
Cytomap19p13.3
Gene Typeprotein-coding
GO ID

GO:0000375

UniProtAcc

P26599


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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
5725PTBP1HTA11_3410_2000001011HumanColorectumAD6.14e-032.51e-010.0155
5725PTBP1HTA11_2487_2000001011HumanColorectumSER5.08e-054.21e-01-0.1808
5725PTBP1HTA11_1938_2000001011HumanColorectumAD5.60e-086.11e-01-0.0811
5725PTBP1HTA11_347_2000001011HumanColorectumAD2.54e-165.81e-01-0.1954
5725PTBP1HTA11_411_2000001011HumanColorectumSER4.34e-048.47e-01-0.2602
5725PTBP1HTA11_696_2000001011HumanColorectumAD2.21e-106.08e-01-0.1464
5725PTBP1HTA11_1391_2000001011HumanColorectumAD5.05e-138.09e-01-0.059
5725PTBP1HTA11_2992_2000001011HumanColorectumSER1.23e-035.24e-01-0.1706
5725PTBP1HTA11_866_3004761011HumanColorectumAD1.14e-065.16e-010.096
5725PTBP1HTA11_4255_2000001011HumanColorectumSER1.18e-026.75e-010.0446
5725PTBP1HTA11_7663_2000001011HumanColorectumSER4.82e-025.61e-010.0131
5725PTBP1HTA11_10623_2000001011HumanColorectumAD1.68e-046.59e-01-0.0177
5725PTBP1HTA11_6801_2000001011HumanColorectumSER6.19e-099.92e-010.0171
5725PTBP1HTA11_7696_3000711011HumanColorectumAD7.61e-177.17e-010.0674
5725PTBP1HTA11_7469_2000001011HumanColorectumAD1.73e-047.95e-01-0.0124
5725PTBP1HTA11_99999970781_79442HumanColorectumMSS8.32e-167.62e-010.294
5725PTBP1HTA11_99999965062_69753HumanColorectumMSI-H7.43e-061.13e+000.3487
5725PTBP1HTA11_99999965104_69814HumanColorectumMSS2.18e-241.15e+000.281
5725PTBP1HTA11_99999971662_82457HumanColorectumMSS8.57e-147.86e-010.3859
5725PTBP1HTA11_99999973899_84307HumanColorectumMSS5.45e-055.55e-010.2585
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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
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.

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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:0016032ColorectumADviral process168/3918415/187234.67e-203.66e-17168
GO:0008380ColorectumADRNA splicing169/3918434/187233.59e-182.04e-15169
GO:0000377ColorectumADRNA splicing, via transesterification reactions with bulged adenosine as nucleophile130/3918320/187235.88e-162.16e-13130
GO:0000398ColorectumADmRNA splicing, via spliceosome130/3918320/187235.88e-162.16e-13130
GO:0000375ColorectumADRNA splicing, via transesterification reactions131/3918324/187237.11e-162.22e-13131
GO:1903311ColorectumADregulation of mRNA metabolic process117/3918288/187231.69e-144.23e-12117
GO:0043484ColorectumADregulation of RNA splicing70/3918148/187236.47e-131.16e-1070
GO:0048024ColorectumADregulation of mRNA splicing, via spliceosome50/3918101/187231.62e-101.56e-0850
GO:0050684ColorectumADregulation of mRNA processing61/3918137/187234.23e-103.58e-0861
GO:0019080ColorectumADviral gene expression42/391894/187231.90e-078.02e-0642
GO:0000380ColorectumADalternative mRNA splicing, via spliceosome33/391877/187231.13e-052.55e-0433
GO:0016311ColorectumADdephosphorylation123/3918417/187231.84e-053.82e-04123
GO:1903312ColorectumADnegative regulation of mRNA metabolic process37/391892/187231.95e-054.01e-0437
GO:0033119ColorectumADnegative regulation of RNA splicing15/391825/187232.37e-054.62e-0415
GO:0000381ColorectumADregulation of alternative mRNA splicing, via spliceosome27/391860/187232.41e-054.66e-0427
GO:0006470ColorectumADprotein dephosphorylation88/3918281/187232.56e-054.89e-0488
GO:0035303ColorectumADregulation of dephosphorylation46/3918128/187236.20e-051.04e-0346
GO:0075522ColorectumADIRES-dependent viral translational initiation8/391811/187233.26e-043.85e-038
GO:0019081ColorectumADviral translation10/391816/187233.64e-044.22e-0310
GO:0035304ColorectumADregulation of protein dephosphorylation33/391890/187234.23e-044.77e-0333
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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
PTBP1SNVMissense_Mutationrs140010693c.47N>Tp.Ser16Phep.S16FP26599protein_codingdeleterious(0)benign(0.062)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
PTBP1SNVMissense_Mutationnovelc.1117G>Ap.Glu373Lysp.E373KP26599protein_codingdeleterious(0.03)benign(0.063)TCGA-AC-A5XS-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyfemaraSD
PTBP1SNVMissense_Mutationc.1365C>Gp.Asp455Glup.D455EP26599protein_codingdeleterious(0)probably_damaging(0.974)TCGA-AN-A0XR-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
PTBP1SNVMissense_Mutationc.1282A>Gp.Lys428Glup.K428EP26599protein_codingdeleterious(0)probably_damaging(0.946)TCGA-AR-A24H-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
PTBP1SNVMissense_Mutationc.1604T>Gp.Ile535Serp.I535SP26599protein_codingdeleterious(0)probably_damaging(0.995)TCGA-BH-A0W7-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxotereCR
PTBP1SNVMissense_Mutationc.961N>Gp.Gln321Glup.Q321EP26599protein_codingtolerated(0.25)benign(0.015)TCGA-D8-A1JA-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinPD
PTBP1SNVMissense_Mutationnovelc.80N>Ap.Gly27Glup.G27EP26599protein_codingdeleterious(0.02)benign(0.434)TCGA-2W-A8YY-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
PTBP1SNVMissense_Mutationc.1656N>Gp.Phe552Leup.F552LP26599protein_codingdeleterious(0)probably_damaging(1)TCGA-IR-A3LK-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycisplatinPD
PTBP1insertionFrame_Shift_Insnovelc.653dupAp.Asn219GlufsTer52p.N219Efs*52P26599protein_codingTCGA-EA-A3HU-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
PTBP1SNVMissense_Mutationc.785G>Ap.Ser262Asnp.S262NP26599protein_codingtolerated(0.77)benign(0)TCGA-AA-3663-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownSD
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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
5725PTBP1DRUGGABLE GENOMEMMV085203CHEMBL586031
5725PTBP1DRUGGABLE GENOMEDNDI1417941CHEMBL2095095
5725PTBP1DRUGGABLE GENOMEGNF-PF-4418CHEMBL604321
5725PTBP1DRUGGABLE GENOMESJ000154295CHEMBL578502
5725PTBP1DRUGGABLE GENOMEELLIPTECINEELLIPTECINE
5725PTBP1DRUGGABLE GENOMESJ000044511CHEMBL592124
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