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: IDH1

Gene summary for IDH1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

IDH1

Gene ID

3417

Gene nameisocitrate dehydrogenase (NADP(+)) 1
Gene AliasHEL-216
Cytomap2q34
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

O75874


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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
3417IDH1HTA11_78_2000001011HumanColorectumAD7.60e-077.30e-01-0.1088
3417IDH1HTA11_347_2000001011HumanColorectumAD6.76e-179.29e-01-0.1954
3417IDH1HTA11_99999970781_79442HumanColorectumMSS8.70e-219.46e-010.294
3417IDH1HTA11_99999971662_82457HumanColorectumMSS4.74e-074.98e-010.3859
3417IDH1F007HumanColorectumFAP1.08e-03-2.19e-010.1176
3417IDH1A002-C-010HumanColorectumFAP4.74e-02-1.78e-010.242
3417IDH1A001-C-207HumanColorectumFAP3.09e-03-2.09e-010.1278
3417IDH1A015-C-203HumanColorectumFAP8.12e-13-2.70e-01-0.1294
3417IDH1A015-C-204HumanColorectumFAP3.87e-03-1.68e-01-0.0228
3417IDH1A014-C-040HumanColorectumFAP5.09e-04-3.40e-01-0.1184
3417IDH1A002-C-201HumanColorectumFAP1.23e-11-2.70e-010.0324
3417IDH1A002-C-203HumanColorectumFAP7.80e-06-1.71e-010.2786
3417IDH1A001-C-119HumanColorectumFAP1.33e-06-2.79e-01-0.1557
3417IDH1A001-C-108HumanColorectumFAP6.19e-11-2.66e-01-0.0272
3417IDH1A002-C-205HumanColorectumFAP5.81e-15-3.12e-01-0.1236
3417IDH1A001-C-104HumanColorectumFAP1.84e-03-2.34e-010.0184
3417IDH1A015-C-005HumanColorectumFAP8.72e-07-2.46e-01-0.0336
3417IDH1A015-C-006HumanColorectumFAP1.54e-08-2.51e-01-0.0994
3417IDH1A015-C-106HumanColorectumFAP3.39e-08-2.78e-01-0.0511
3417IDH1A002-C-114HumanColorectumFAP4.44e-09-2.46e-01-0.1561
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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
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:0006091ColorectumADgeneration of precursor metabolites and energy209/3918490/187233.17e-286.61e-25209
GO:0009060ColorectumADaerobic respiration108/3918189/187239.14e-281.43e-24108
GO:0045333ColorectumADcellular respiration119/3918230/187233.21e-254.02e-22119
GO:0015980ColorectumADenergy derivation by oxidation of organic compounds143/3918318/187232.78e-222.49e-19143
GO:0006979ColorectumADresponse to oxidative stress145/3918446/187235.16e-093.23e-07145
GO:0006099ColorectumADtricarboxylic acid cycle19/391830/187235.82e-072.09e-0519
GO:0048545ColorectumADresponse to steroid hormone104/3918339/187231.33e-052.90e-04104
GO:0006066ColorectumADalcohol metabolic process106/3918353/187233.02e-055.57e-04106
GO:0016042ColorectumADlipid catabolic process97/3918320/187234.31e-057.56e-0497
GO:0044262ColorectumADcellular carbohydrate metabolic process87/3918283/187236.00e-051.01e-0387
GO:0006790ColorectumADsulfur compound metabolic process101/3918339/187236.46e-051.07e-03101
GO:0044242ColorectumADcellular lipid catabolic process66/3918214/187233.96e-044.50e-0366
GO:0006575ColorectumADcellular modified amino acid metabolic process59/3918188/187234.80e-045.27e-0359
GO:0043648ColorectumADdicarboxylic acid metabolic process34/391896/187237.22e-047.28e-0334
GO:0061458ColorectumADreproductive system development116/3918427/187231.11e-031.01e-02116
GO:0048608ColorectumADreproductive structure development114/3918424/187231.78e-031.47e-02114
GO:0006081ColorectumADcellular aldehyde metabolic process22/391860/187233.64e-032.60e-0222
GO:0006644ColorectumADphospholipid metabolic process101/3918383/187235.80e-033.67e-02101
GO:00090602ColorectumMSSaerobic respiration98/3467189/187233.35e-251.05e-2198
GO:00060912ColorectumMSSgeneration of precursor metabolites and energy186/3467490/187231.14e-242.15e-21186
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa01200ColorectumADCarbon metabolism55/2092115/84655.53e-088.42e-075.37e-0755
hsa00020ColorectumADCitrate cycle (TCA cycle)20/209230/84651.43e-061.77e-051.13e-0520
hsa05230ColorectumADCentral carbon metabolism in cancer33/209270/84653.61e-053.19e-042.03e-0433
hsa00480ColorectumADGlutathione metabolism23/209257/84656.52e-032.76e-021.76e-0223
hsa01230ColorectumADBiosynthesis of amino acids28/209275/84659.99e-033.89e-022.48e-0228
hsa012001ColorectumADCarbon metabolism55/2092115/84655.53e-088.42e-075.37e-0755
hsa000201ColorectumADCitrate cycle (TCA cycle)20/209230/84651.43e-061.77e-051.13e-0520
hsa052301ColorectumADCentral carbon metabolism in cancer33/209270/84653.61e-053.19e-042.03e-0433
hsa004801ColorectumADGlutathione metabolism23/209257/84656.52e-032.76e-021.76e-0223
hsa012301ColorectumADBiosynthesis of amino acids28/209275/84659.99e-033.89e-022.48e-0228
hsa012004ColorectumMSSCarbon metabolism43/1875115/84651.37e-041.17e-037.19e-0443
hsa000204ColorectumMSSCitrate cycle (TCA cycle)16/187530/84651.84e-041.47e-039.00e-0416
hsa004802ColorectumMSSGlutathione metabolism22/187557/84653.58e-031.64e-021.01e-0222
hsa052304ColorectumMSSCentral carbon metabolism in cancer25/187570/84656.50e-032.64e-021.62e-0225
hsa012005ColorectumMSSCarbon metabolism43/1875115/84651.37e-041.17e-037.19e-0443
hsa000205ColorectumMSSCitrate cycle (TCA cycle)16/187530/84651.84e-041.47e-039.00e-0416
hsa004803ColorectumMSSGlutathione metabolism22/187557/84653.58e-031.64e-021.01e-0222
hsa052305ColorectumMSSCentral carbon metabolism in cancer25/187570/84656.50e-032.64e-021.62e-0225
hsa012006ColorectumFAPCarbon metabolism38/1404115/84651.04e-051.44e-048.76e-0538
hsa052306ColorectumFAPCentral carbon metabolism in cancer23/140470/84656.12e-044.26e-032.59e-0323
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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
IDH1SNVMissense_Mutationc.251A>Cp.Glu84Alap.E84AO75874protein_codingtolerated_low_confidence(0.08)possibly_damaging(0.459)TCGA-AX-A063-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
IDH1SNVMissense_Mutationnovelc.556G>Tp.Asp186Tyrp.D186YO75874protein_codingdeleterious_low_confidence(0)probably_damaging(0.997)TCGA-AX-A2HC-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapypaclitaxelPD
IDH1SNVMissense_Mutationrs747419787c.355N>Tp.Arg119Trpp.R119WO75874protein_codingdeleterious_low_confidence(0.01)benign(0.024)TCGA-B5-A11E-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
IDH1SNVMissense_Mutationnovelc.499N>Cp.Tyr167Hisp.Y167HO75874protein_codingtolerated_low_confidence(0.92)benign(0.015)TCGA-B5-A3FA-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
IDH1SNVMissense_Mutationc.974N>Tp.Thr325Metp.T325MO75874protein_codingdeleterious_low_confidence(0)probably_damaging(1)TCGA-B5-A3FC-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
IDH1SNVMissense_Mutationnovelc.1069N>Gp.Asn357Aspp.N357DO75874protein_codingtolerated_low_confidence(0.29)benign(0)TCGA-BG-A222-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
IDH1SNVMissense_Mutationc.274N>Cp.Trp92Argp.W92RO75874protein_codingdeleterious_low_confidence(0)probably_damaging(1)TCGA-E6-A1LZ-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIChemotherapycarboplatinSD
IDH1SNVMissense_Mutationnovelc.492N>Tp.Lys164Asnp.K164NO75874protein_codingdeleterious_low_confidence(0.02)benign(0.082)TCGA-EC-A1QX-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIChemotherapycyclophosphamidePD
IDH1SNVMissense_Mutationnovelc.1037N>Gp.Leu346Argp.L346RO75874protein_codingdeleterious_low_confidence(0)probably_damaging(0.999)TCGA-EO-A22U-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
IDH1SNVMissense_Mutationnovelc.383T>Gp.Ile128Serp.I128SO75874protein_codingdeleterious_low_confidence(0)probably_damaging(1)TCGA-EO-A22X-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVUnspecificCarboplatinComplete Response
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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
3417IDH1ENZYME, CLINICALLY ACTIONABLEBPTES21045145
3417IDH1ENZYME, CLINICALLY ACTIONABLEGNF-PF-67CHEMBL578512
3417IDH1ENZYME, CLINICALLY ACTIONABLEBAY143603228232670
3417IDH1ENZYME, CLINICALLY ACTIONABLECP-55940CP-55940
3417IDH1ENZYME, CLINICALLY ACTIONABLEBI-87E7CHEMBL523200
3417IDH1ENZYME, CLINICALLY ACTIONABLE1-BENZYLMALEIMIDECHEMBL388979
3417IDH1ENZYME, CLINICALLY ACTIONABLEVENETOCLAXVENETOCLAX30725494
3417IDH1ENZYME, CLINICALLY ACTIONABLECANDIDINCANDIDIN
3417IDH1ENZYME, CLINICALLY ACTIONABLESANGUINARIUM CHLORIDESANGUINARIUM CHLORIDE
3417IDH1ENZYME, CLINICALLY ACTIONABLEDNDI1318477CHEMBL428064
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