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: PGM1

Gene summary for PGM1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PGM1

Gene ID

5236

Gene namephosphoglucomutase 1
Gene AliasCDG1T
Cytomap1p31.3
Gene Typeprotein-coding
GO ID

GO:0005975

UniProtAcc

B7Z6C2


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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
5236PGM1HTA11_347_2000001011HumanColorectumAD7.80e-197.63e-01-0.1954
5236PGM1HTA11_1391_2000001011HumanColorectumAD5.48e-076.12e-01-0.059
5236PGM1F007HumanColorectumFAP3.74e-02-2.71e-010.1176
5236PGM1A001-C-207HumanColorectumFAP3.15e-03-3.04e-010.1278
5236PGM1A015-C-203HumanColorectumFAP6.21e-17-3.12e-01-0.1294
5236PGM1A015-C-204HumanColorectumFAP3.38e-02-2.37e-01-0.0228
5236PGM1A002-C-201HumanColorectumFAP1.81e-07-3.02e-010.0324
5236PGM1A002-C-203HumanColorectumFAP4.80e-06-2.84e-010.2786
5236PGM1A001-C-119HumanColorectumFAP4.29e-05-3.61e-01-0.1557
5236PGM1A001-C-108HumanColorectumFAP2.32e-15-3.22e-01-0.0272
5236PGM1A002-C-205HumanColorectumFAP2.77e-10-3.56e-01-0.1236
5236PGM1A001-C-104HumanColorectumFAP3.09e-06-2.88e-010.0184
5236PGM1A015-C-005HumanColorectumFAP7.75e-05-3.47e-01-0.0336
5236PGM1A015-C-006HumanColorectumFAP1.25e-07-3.76e-01-0.0994
5236PGM1A015-C-106HumanColorectumFAP2.38e-05-2.23e-01-0.0511
5236PGM1A002-C-114HumanColorectumFAP1.06e-07-3.41e-01-0.1561
5236PGM1A015-C-104HumanColorectumFAP2.62e-18-3.17e-01-0.1899
5236PGM1A001-C-014HumanColorectumFAP5.38e-11-3.18e-010.0135
5236PGM1A002-C-016HumanColorectumFAP9.82e-11-3.03e-010.0521
5236PGM1A015-C-002HumanColorectumFAP1.05e-08-4.20e-01-0.0763
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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
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:0046034ColorectumADATP metabolic process142/3918277/187232.64e-298.26e-26142
GO:0006091ColorectumADgeneration of precursor metabolites and energy209/3918490/187233.17e-286.61e-25209
GO:0009150ColorectumADpurine ribonucleotide metabolic process142/3918368/187234.29e-151.17e-12142
GO:0006163ColorectumADpurine nucleotide metabolic process149/3918396/187231.08e-142.80e-12149
GO:0072521ColorectumADpurine-containing compound metabolic process153/3918416/187234.34e-141.01e-11153
GO:0009259ColorectumADribonucleotide metabolic process144/3918385/187235.25e-141.13e-11144
GO:0019693ColorectumADribose phosphate metabolic process145/3918396/187233.01e-135.71e-11145
GO:0009117ColorectumADnucleotide metabolic process168/3918489/187232.20e-123.36e-10168
GO:0006753ColorectumADnucleoside phosphate metabolic process169/3918497/187234.99e-126.98e-10169
GO:0009135ColorectumADpurine nucleoside diphosphate metabolic process47/3918103/187231.61e-089.22e-0747
GO:0009179ColorectumADpurine ribonucleoside diphosphate metabolic process47/3918103/187231.61e-089.22e-0747
GO:0006090ColorectumADpyruvate metabolic process47/3918106/187234.85e-082.55e-0647
GO:0009185ColorectumADribonucleoside diphosphate metabolic process47/3918106/187234.85e-082.55e-0647
GO:0046031ColorectumADADP metabolic process41/391890/187231.37e-076.42e-0641
GO:0006096ColorectumADglycolytic process38/391881/187231.52e-076.78e-0638
GO:0006757ColorectumADATP generation from ADP38/391882/187232.26e-079.37e-0638
GO:0009132ColorectumADnucleoside diphosphate metabolic process49/3918124/187231.75e-065.31e-0549
GO:0046939ColorectumADnucleotide phosphorylation42/3918101/187231.99e-065.92e-0542
GO:0016052ColorectumADcarbohydrate catabolic process56/3918154/187237.01e-061.73e-0456
GO:0006165ColorectumADnucleoside diphosphate phosphorylation40/391899/187238.02e-061.93e-0440
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa00010ColorectumADGlycolysis / Gluconeogenesis34/209267/84653.63e-064.34e-052.77e-0534
hsa000101ColorectumADGlycolysis / Gluconeogenesis34/209267/84653.63e-064.34e-052.77e-0534
hsa000106ColorectumFAPGlycolysis / Gluconeogenesis24/140467/84651.05e-049.46e-045.76e-0424
hsa01250ColorectumFAPBiosynthesis of nucleotide sugars13/140437/84654.79e-031.91e-021.16e-0213
hsa000107ColorectumFAPGlycolysis / Gluconeogenesis24/140467/84651.05e-049.46e-045.76e-0424
hsa012501ColorectumFAPBiosynthesis of nucleotide sugars13/140437/84654.79e-031.91e-021.16e-0213
hsa012502ColorectumCRCBiosynthesis of nucleotide sugars12/109137/84651.66e-031.20e-028.16e-0312
hsa012503ColorectumCRCBiosynthesis of nucleotide sugars12/109137/84651.66e-031.20e-028.16e-0312
hsa012505EsophagusESCCBiosynthesis of nucleotide sugars28/420537/84651.10e-033.42e-031.75e-0328
hsa005202EsophagusESCCAmino sugar and nucleotide sugar metabolism35/420549/84651.60e-034.88e-032.50e-0335
hsa0001016EsophagusESCCGlycolysis / Gluconeogenesis42/420567/84652.15e-024.78e-022.45e-0242
hsa0125012EsophagusESCCBiosynthesis of nucleotide sugars28/420537/84651.10e-033.42e-031.75e-0328
hsa0052011EsophagusESCCAmino sugar and nucleotide sugar metabolism35/420549/84651.60e-034.88e-032.50e-0335
hsa0001017EsophagusESCCGlycolysis / Gluconeogenesis42/420567/84652.15e-024.78e-022.45e-0242
hsa000109LiverCirrhoticGlycolysis / Gluconeogenesis32/253067/84651.50e-037.80e-034.81e-0332
hsa00030LiverCirrhoticPentose phosphate pathway16/253030/84656.04e-032.12e-021.30e-0216
hsa0001012LiverCirrhoticGlycolysis / Gluconeogenesis32/253067/84651.50e-037.80e-034.81e-0332
hsa000301LiverCirrhoticPentose phosphate pathway16/253030/84656.04e-032.12e-021.30e-0216
hsa0001022LiverHCCGlycolysis / Gluconeogenesis43/402067/84654.26e-031.29e-027.15e-0343
hsa000302LiverHCCPentose phosphate pathway21/402030/84651.06e-022.71e-021.51e-0221
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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
PGM1SNVMissense_Mutationnovelc.231N>Gp.Ile77Metp.I77MP36871protein_codingtolerated(1)benign(0.04)TCGA-AC-A6IW-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PGM1SNVMissense_Mutationnovelc.1106C>Tp.Ala369Valp.A369VP36871protein_codingtolerated(0.15)benign(0.028)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PGM1SNVMissense_Mutationrs748304901c.716N>Ap.Arg239Hisp.R239HP36871protein_codingtolerated(0.56)benign(0.033)TCGA-AN-A0FZ-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
PGM1SNVMissense_Mutationnovelc.1198N>Tp.Gly400Cysp.G400CP36871protein_codingdeleterious(0)probably_damaging(0.999)TCGA-D8-A73W-01Breastbreast invasive carcinomaFemale>=65III/IVHormone TherapytamoxiphenPD
PGM1insertionNonsense_Mutationnovelc.116_117insCTTCAAATACAAAGGACTTAAACTGCTTCCCTAAAAACp.Leu40PhefsTer11p.L40Ffs*11P36871protein_codingTCGA-AN-A03X-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PGM1deletionFrame_Shift_Delnovelc.1517delAp.Gln506ArgfsTer17p.Q506Rfs*17P36871protein_codingTCGA-EW-A2FV-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydocetaxelSD
PGM1SNVMissense_Mutationc.1233G>Tp.Trp411Cysp.W411CP36871protein_codingdeleterious(0)probably_damaging(1)TCGA-DS-A1OC-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapygemcitabineSD
PGM1SNVMissense_Mutationrs201303497c.1366N>Ap.Ala456Thrp.A456TP36871protein_codingdeleterious(0.03)possibly_damaging(0.786)TCGA-EA-A3HS-01Cervixcervical & endocervical cancerFemale<65I/IIUnknownUnknownSD
PGM1SNVMissense_Mutationnovelc.205N>Cp.Asp69Hisp.D69HP36871protein_codingdeleterious(0.01)benign(0.015)TCGA-VS-A8EK-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycisplatinPD
PGM1SNVMissense_Mutationc.391N>Gp.Ile131Valp.I131VP36871protein_codingtolerated(0.22)benign(0.168)TCGA-AA-3877-01Colorectumcolon 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
5236PGM1ENZYMEacetaldehydeACETALDEHYDE31002879
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