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: PABPC4

Gene summary for PABPC4

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PABPC4

Gene ID

8761

Gene namepoly(A) binding protein cytoplasmic 4
Gene AliasAPP-1
Cytomap1p34.3
Gene Typeprotein-coding
GO ID

GO:0002376

UniProtAcc

Q13310


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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
8761PABPC4HTA11_347_2000001011HumanColorectumAD7.46e-031.67e-01-0.1954
8761PABPC4HTA11_866_3004761011HumanColorectumAD9.34e-053.58e-010.096
8761PABPC4HTA11_7696_3000711011HumanColorectumAD3.29e-065.14e-010.0674
8761PABPC4HTA11_6818_2000001021HumanColorectumAD2.64e-065.95e-010.0588
8761PABPC4HTA11_99999970781_79442HumanColorectumMSS5.13e-136.62e-010.294
8761PABPC4HTA11_99999965104_69814HumanColorectumMSS5.18e-075.19e-010.281
8761PABPC4HTA11_99999971662_82457HumanColorectumMSS5.41e-311.07e+000.3859
8761PABPC4HTA11_99999974143_84620HumanColorectumMSS2.91e-064.62e-010.3005
8761PABPC4A015-C-203HumanColorectumFAP3.48e-072.25e-01-0.1294
8761PABPC4A014-C-040HumanColorectumFAP1.79e-057.54e-01-0.1184
8761PABPC4A001-C-108HumanColorectumFAP3.16e-02-4.82e-02-0.0272
8761PABPC4A002-C-021HumanColorectumFAP1.96e-022.72e-010.1171
8761PABPC4A002-C-205HumanColorectumFAP1.30e-028.94e-02-0.1236
8761PABPC4A015-C-104HumanColorectumFAP5.02e-05-2.92e-02-0.1899
8761PABPC4A002-C-016HumanColorectumFAP4.02e-031.85e-010.0521
8761PABPC4A002-C-116HumanColorectumFAP1.45e-113.10e-01-0.0452
8761PABPC4AEH-subject2HumanEndometriumAEH3.42e-03-3.60e-02-0.2525
8761PABPC4AEH-subject3HumanEndometriumAEH2.31e-06-2.58e-01-0.2576
8761PABPC4EEC-subject1HumanEndometriumEEC3.41e-09-3.26e-01-0.2682
8761PABPC4EEC-subject2HumanEndometriumEEC5.33e-04-1.61e-01-0.2607
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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:1903311ColorectumADregulation of mRNA metabolic process117/3918288/187231.69e-144.23e-12117
GO:0006401ColorectumADRNA catabolic process102/3918278/187238.64e-106.76e-08102
GO:0044270ColorectumADcellular nitrogen compound catabolic process147/3918451/187233.35e-092.23e-07147
GO:0046700ColorectumADheterocycle catabolic process145/3918445/187234.37e-092.84e-07145
GO:0006402ColorectumADmRNA catabolic process87/3918232/187234.40e-092.84e-0787
GO:0034655ColorectumADnucleobase-containing compound catabolic process133/3918407/187231.56e-089.12e-07133
GO:0019439ColorectumADaromatic compound catabolic process146/3918467/187237.48e-083.84e-06146
GO:1901361ColorectumADorganic cyclic compound catabolic process153/3918495/187238.23e-084.18e-06153
GO:0061013ColorectumADregulation of mRNA catabolic process64/3918166/187231.44e-076.59e-0664
GO:0043487ColorectumADregulation of RNA stability63/3918170/187239.17e-073.12e-0563
GO:0030099ColorectumADmyeloid cell differentiation119/3918381/187231.24e-064.01e-05119
GO:0043488ColorectumADregulation of mRNA stability59/3918158/187231.50e-064.66e-0559
GO:0042060ColorectumADwound healing128/3918422/187232.73e-067.89e-05128
GO:0050878ColorectumADregulation of body fluid levels108/3918379/187232.54e-043.20e-03108
GO:19033112ColorectumMSSregulation of mRNA metabolic process115/3467288/187231.23e-176.41e-15115
GO:00064012ColorectumMSSRNA catabolic process102/3467278/187235.07e-131.02e-10102
GO:00064022ColorectumMSSmRNA catabolic process89/3467232/187238.70e-131.60e-1089
GO:00442702ColorectumMSScellular nitrogen compound catabolic process141/3467451/187232.95e-113.83e-09141
GO:00467002ColorectumMSSheterocycle catabolic process139/3467445/187234.37e-115.05e-09139
GO:00346552ColorectumMSSnucleobase-containing compound catabolic process129/3467407/187237.48e-118.18e-09129
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa03015ColorectumADmRNA surveillance pathway35/209297/84657.95e-033.13e-022.00e-0235
hsa030151ColorectumADmRNA surveillance pathway35/209297/84657.95e-033.13e-022.00e-0235
hsa030152ColorectumFAPmRNA surveillance pathway26/140497/84657.11e-032.64e-021.60e-0226
hsa030153ColorectumFAPmRNA surveillance pathway26/140497/84657.11e-032.64e-021.60e-0226
hsa030187EndometriumEECRNA degradation20/123779/84658.36e-033.88e-022.89e-0220
hsa0301812EndometriumEECRNA degradation20/123779/84658.36e-033.88e-022.89e-0220
hsa0301824EsophagusESCCRNA degradation62/420579/84651.18e-079.39e-074.81e-0762
hsa0301524EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa0301834EsophagusESCCRNA degradation62/420579/84651.18e-079.39e-074.81e-0762
hsa0301534EsophagusESCCmRNA surveillance pathway72/420597/84656.12e-074.10e-062.10e-0672
hsa03018LiverCirrhoticRNA degradation44/253079/84651.43e-061.65e-051.02e-0544
hsa030154LiverCirrhoticmRNA surveillance pathway46/253097/84651.92e-041.30e-038.03e-0446
hsa030181LiverCirrhoticRNA degradation44/253079/84651.43e-061.65e-051.02e-0544
hsa0301511LiverCirrhoticmRNA surveillance pathway46/253097/84651.92e-041.30e-038.03e-0446
hsa030182LiverHCCRNA degradation58/402079/84652.29e-062.19e-051.22e-0558
hsa0301521LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa030183LiverHCCRNA degradation58/402079/84652.29e-062.19e-051.22e-0558
hsa0301531LiverHCCmRNA surveillance pathway66/402097/84653.16e-051.88e-041.04e-0466
hsa030158Oral cavityOSCCmRNA surveillance pathway75/370497/84651.30e-112.01e-101.02e-1075
hsa030189Oral cavityOSCCRNA degradation59/370479/84652.05e-081.91e-079.70e-0859
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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
PABPC4SNVMissense_Mutationnovelc.110N>Ap.Val37Glup.V37EQ13310protein_codingdeleterious(0)probably_damaging(0.952)TCGA-A2-A4RW-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
PABPC4SNVMissense_Mutationnovelc.922G>Ap.Glu308Lysp.E308KQ13310protein_codingtolerated(0.06)probably_damaging(0.911)TCGA-A7-A56D-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
PABPC4SNVMissense_Mutationc.1702N>Cp.Glu568Glnp.E568QQ13310protein_codingdeleterious(0.03)possibly_damaging(0.63)TCGA-A8-A085-01Breastbreast invasive carcinomaMale<65I/IIHormone TherapytamoxiphenSD
PABPC4SNVMissense_Mutationnovelc.1343N>Tp.Gly448Valp.G448VQ13310protein_codingtolerated(0.15)benign(0.003)TCGA-AN-A03X-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PABPC4SNVMissense_Mutationc.1252N>Ap.Gly418Argp.G418RQ13310protein_codingtolerated(0.68)benign(0.019)TCGA-C8-A1HJ-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PABPC4SNVMissense_Mutationnovelc.1202T>Cp.Phe401Serp.F401SQ13310protein_codingtolerated(0.1)benign(0.019)TCGA-E2-A15M-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
PABPC4deletionIn_Frame_Delc.123_146delNNNNNNNNNNNNNNNNNNNNNNNNp.Val42_Arg49delp.V42_R49delQ13310protein_codingTCGA-GM-A2DH-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapytaxolCR
PABPC4SNVMissense_Mutationc.1145N>Gp.Tyr382Cysp.Y382CQ13310protein_codingdeleterious(0)possibly_damaging(0.682)TCGA-C5-A3HL-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
PABPC4SNVMissense_Mutationnovelc.919G>Tp.Asp307Tyrp.D307YQ13310protein_codingdeleterious(0)probably_damaging(0.996)TCGA-C5-A8ZZ-01Cervixcervical & endocervical cancerFemale<65I/IIUnspecificCisplatinSD
PABPC4SNVMissense_Mutationc.106N>Tp.Pro36Serp.P36SQ13310protein_codingtolerated(0.06)benign(0.314)TCGA-AA-3492-01Colorectumcolon adenocarcinomaFemale>=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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