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: PAF1

Gene summary for PAF1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PAF1

Gene ID

54623

Gene namePAF1 homolog, Paf1/RNA polymerase II complex component
Gene AliasF23149_1
Cytomap19q13.2
Gene Typeprotein-coding
GO ID

GO:0000122

UniProtAcc

Q8N7H5


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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
54623PAF1LZE4THumanEsophagusESCC2.35e-102.85e-010.0811
54623PAF1LZE7THumanEsophagusESCC6.25e-074.52e-010.0667
54623PAF1LZE8THumanEsophagusESCC3.60e-142.37e-010.067
54623PAF1LZE20THumanEsophagusESCC4.50e-05-2.04e-020.0662
54623PAF1LZE22THumanEsophagusESCC5.57e-072.63e-010.068
54623PAF1LZE24THumanEsophagusESCC1.03e-175.06e-010.0596
54623PAF1LZE21THumanEsophagusESCC3.29e-051.87e-010.0655
54623PAF1LZE6THumanEsophagusESCC1.99e-102.19e-010.0845
54623PAF1P1T-EHumanEsophagusESCC1.06e-119.73e-010.0875
54623PAF1P2T-EHumanEsophagusESCC3.36e-255.34e-010.1177
54623PAF1P4T-EHumanEsophagusESCC1.15e-215.15e-010.1323
54623PAF1P5T-EHumanEsophagusESCC6.83e-131.96e-010.1327
54623PAF1P8T-EHumanEsophagusESCC3.63e-338.67e-010.0889
54623PAF1P9T-EHumanEsophagusESCC8.69e-196.26e-020.1131
54623PAF1P10T-EHumanEsophagusESCC2.53e-274.87e-010.116
54623PAF1P11T-EHumanEsophagusESCC4.35e-166.07e-010.1426
54623PAF1P12T-EHumanEsophagusESCC2.92e-306.29e-010.1122
54623PAF1P15T-EHumanEsophagusESCC2.61e-245.29e-010.1149
54623PAF1P16T-EHumanEsophagusESCC8.13e-202.43e-010.1153
54623PAF1P17T-EHumanEsophagusESCC5.58e-083.81e-010.1278
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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
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:001657015EsophagusESCChistone modification323/8552463/187232.61e-267.88e-24323
GO:1903311110EsophagusESCCregulation of mRNA metabolic process210/8552288/187233.25e-215.56e-19210
GO:003450418EsophagusESCCprotein localization to nucleus211/8552290/187234.06e-216.60e-19211
GO:0050684110EsophagusESCCregulation of mRNA processing109/8552137/187233.51e-162.59e-14109
GO:000635414EsophagusESCCDNA-templated transcription, elongation76/855291/187238.35e-144.11e-1276
GO:190198713EsophagusESCCregulation of cell cycle phase transition242/8552390/187233.86e-111.26e-09242
GO:001605517EsophagusESCCWnt signaling pathway268/8552444/187232.32e-106.58e-09268
GO:019873817EsophagusESCCcell-cell signaling by wnt269/8552446/187232.41e-106.79e-09269
GO:00434143EsophagusESCCmacromolecule methylation199/8552316/187233.44e-109.57e-09199
GO:190331316EsophagusESCCpositive regulation of mRNA metabolic process87/8552118/187235.10e-101.32e-0887
GO:004578710EsophagusESCCpositive regulation of cell cycle196/8552313/187239.27e-102.24e-08196
GO:0030099111EsophagusESCCmyeloid cell differentiation232/8552381/187231.22e-092.90e-08232
GO:000636814EsophagusESCCtranscription elongation from RNA polymerase II promoter56/855269/187231.40e-093.30e-0856
GO:003105614EsophagusESCCregulation of histone modification106/8552152/187231.52e-093.55e-08106
GO:00322592EsophagusESCCmethylation222/8552364/187232.26e-095.09e-08222
GO:00065136EsophagusESCCprotein monoubiquitination53/855267/187232.11e-084.03e-0753
GO:001657414EsophagusESCChistone ubiquitination40/855247/187232.40e-084.55e-0740
GO:000632517EsophagusESCCchromatin organization240/8552409/187236.52e-081.14e-06240
GO:009872714EsophagusESCCmaintenance of cell number90/8552134/187233.94e-075.43e-0690
GO:001982714EsophagusESCCstem cell population maintenance88/8552131/187235.23e-076.97e-0688
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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
PAF1SNVMissense_Mutationc.1067T>Cp.Met356Thrp.M356TQ8N7H5protein_codingtolerated(0.11)possibly_damaging(0.647)TCGA-AO-A128-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicinSD
PAF1SNVMissense_Mutationc.79N>Ap.Ser27Thrp.S27TQ8N7H5protein_codingtolerated(0.1)benign(0.214)TCGA-BH-A0HO-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycyclophosphamideSD
PAF1SNVMissense_Mutationc.1099N>Tp.Arg367Trpp.R367WQ8N7H5protein_codingdeleterious(0)probably_damaging(0.999)TCGA-C5-A1BN-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinPD
PAF1SNVMissense_Mutationc.1234G>Cp.Glu412Glnp.E412QQ8N7H5protein_codingdeleterious(0.05)benign(0.105)TCGA-DG-A2KH-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
PAF1SNVMissense_Mutationc.261N>Gp.Ile87Metp.I87MQ8N7H5protein_codingdeleterious(0)probably_damaging(0.999)TCGA-IR-A3LK-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycisplatinPD
PAF1SNVMissense_Mutationc.499N>Ap.Glu167Lysp.E167KQ8N7H5protein_codingtolerated(0.5)benign(0.082)TCGA-JX-A3Q0-01Cervixcervical & endocervical cancerFemale<65III/IVUnknownUnknownSD
PAF1SNVMissense_Mutationc.1321N>Cp.Glu441Glnp.E441QQ8N7H5protein_codingdeleterious(0.03)possibly_damaging(0.856)TCGA-A6-2686-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
PAF1SNVMissense_Mutationc.526N>Cp.Ile176Leup.I176LQ8N7H5protein_codingdeleterious(0.04)possibly_damaging(0.465)TCGA-AA-3492-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownSD
PAF1SNVMissense_Mutationc.931T>Cp.Tyr311Hisp.Y311HQ8N7H5protein_codingtolerated(0.06)possibly_damaging(0.76)TCGA-AA-3811-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownPD
PAF1SNVMissense_Mutationnovelc.98N>Cp.Val33Alap.V33AQ8N7H5protein_codingdeleterious(0)possibly_damaging(0.726)TCGA-AA-3939-01Colorectumcolon 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
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