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: BCKDHB

Gene summary for BCKDHB

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

BCKDHB

Gene ID

594

Gene namebranched chain keto acid dehydrogenase E1 subunit beta
Gene AliasBCKDE1B
Cytomap6q14.1
Gene Typeprotein-coding
GO ID

GO:0006082

UniProtAcc

A0A140VKB3


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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
594BCKDHBHTA11_3410_2000001011HumanColorectumAD3.38e-09-5.14e-010.0155
594BCKDHBHTA11_3361_2000001011HumanColorectumAD4.23e-05-5.15e-01-0.1207
594BCKDHBHTA11_696_2000001011HumanColorectumAD1.73e-03-3.09e-01-0.1464
594BCKDHBHTA11_866_2000001011HumanColorectumAD1.24e-04-3.77e-01-0.1001
594BCKDHBHTA11_866_3004761011HumanColorectumAD3.21e-08-5.34e-010.096
594BCKDHBHTA11_7696_3000711011HumanColorectumAD3.61e-03-3.41e-010.0674
594BCKDHBHTA11_99999970781_79442HumanColorectumMSS1.96e-02-2.91e-010.294
594BCKDHBHTA11_99999971662_82457HumanColorectumMSS1.71e-02-3.57e-010.3859
594BCKDHBHTA11_99999974143_84620HumanColorectumMSS1.74e-11-4.84e-010.3005
594BCKDHBA001-C-207HumanColorectumFAP6.61e-04-2.70e-010.1278
594BCKDHBA015-C-203HumanColorectumFAP6.07e-36-5.87e-01-0.1294
594BCKDHBA015-C-204HumanColorectumFAP1.92e-07-3.67e-01-0.0228
594BCKDHBA014-C-040HumanColorectumFAP2.57e-05-4.30e-01-0.1184
594BCKDHBA002-C-201HumanColorectumFAP2.58e-16-3.94e-010.0324
594BCKDHBA002-C-203HumanColorectumFAP8.94e-04-1.69e-010.2786
594BCKDHBA001-C-119HumanColorectumFAP9.15e-14-6.21e-01-0.1557
594BCKDHBA001-C-108HumanColorectumFAP1.70e-24-5.73e-01-0.0272
594BCKDHBA002-C-205HumanColorectumFAP4.88e-31-6.50e-01-0.1236
594BCKDHBA001-C-104HumanColorectumFAP2.51e-08-3.83e-010.0184
594BCKDHBA015-C-005HumanColorectumFAP4.14e-07-3.81e-01-0.0336
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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
LungThe 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.AAH: Atypical adenomatous hyperplasia
AIS: Adenocarcinoma in situ
IAC: Invasive lung adenocarcinoma
MIA: Minimally invasive adenocarcinoma
∗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:00442827EsophagusESCCsmall molecule catabolic process201/8552376/187231.35e-036.41e-03201
GO:00090836EsophagusESCCbranched-chain amino acid catabolic process12/855215/187237.31e-032.63e-0212
GO:00090815EsophagusESCCbranched-chain amino acid metabolic process14/855219/187231.27e-024.21e-0214
GO:00463953LiverNAFLDcarboxylic acid catabolic process73/1882236/187234.16e-191.22e-1573
GO:00160544LiverNAFLDorganic acid catabolic process73/1882240/187231.20e-182.34e-1573
GO:00442825LiverNAFLDsmall molecule catabolic process91/1882376/187238.96e-161.31e-1291
GO:0009063LiverNAFLDcellular amino acid catabolic process36/1882110/187236.56e-111.99e-0836
GO:00065203LiverNAFLDcellular amino acid metabolic process63/1882284/187231.14e-092.17e-0763
GO:00316677LiverNAFLDresponse to nutrient levels85/1882474/187238.23e-087.09e-0685
GO:00075844LiverNAFLDresponse to nutrient36/1882174/187232.06e-055.78e-0436
GO:00090813LiverNAFLDbranched-chain amino acid metabolic process8/188219/187232.81e-044.51e-038
GO:00090834LiverNAFLDbranched-chain amino acid catabolic process7/188215/187233.18e-044.95e-037
GO:004428211LiverCirrhoticsmall molecule catabolic process151/4634376/187232.20e-111.34e-09151
GO:001605411LiverCirrhoticorganic acid catabolic process104/4634240/187231.91e-109.53e-09104
GO:004639511LiverCirrhoticcarboxylic acid catabolic process102/4634236/187233.41e-101.63e-08102
GO:003166712LiverCirrhoticresponse to nutrient levels174/4634474/187233.08e-091.27e-07174
GO:00090631LiverCirrhoticcellular amino acid catabolic process49/4634110/187234.47e-067.42e-0549
GO:000652011LiverCirrhoticcellular amino acid metabolic process103/4634284/187238.88e-061.30e-04103
GO:000908111LiverCirrhoticbranched-chain amino acid metabolic process14/463419/187231.00e-051.45e-0414
GO:000758411LiverCirrhoticresponse to nutrient67/4634174/187233.83e-054.59e-0467
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa00280ColorectumADValine, leucine and isoleucine degradation25/209248/84653.97e-053.41e-042.18e-0425
hsa00640ColorectumADPropanoate metabolism18/209232/84651.33e-041.11e-037.08e-0418
hsa002801ColorectumADValine, leucine and isoleucine degradation25/209248/84653.97e-053.41e-042.18e-0425
hsa006401ColorectumADPropanoate metabolism18/209232/84651.33e-041.11e-037.08e-0418
hsa002802ColorectumMSSValine, leucine and isoleucine degradation21/187548/84656.73e-044.51e-032.76e-0321
hsa006404ColorectumMSSPropanoate metabolism15/187532/84651.68e-039.05e-035.55e-0315
hsa002803ColorectumMSSValine, leucine and isoleucine degradation21/187548/84656.73e-044.51e-032.76e-0321
hsa006405ColorectumMSSPropanoate metabolism15/187532/84651.68e-039.05e-035.55e-0315
hsa006406ColorectumFAPPropanoate metabolism15/140432/84656.21e-056.10e-043.71e-0415
hsa002804ColorectumFAPValine, leucine and isoleucine degradation18/140448/84653.94e-043.06e-031.86e-0318
hsa006407ColorectumFAPPropanoate metabolism15/140432/84656.21e-056.10e-043.71e-0415
hsa002805ColorectumFAPValine, leucine and isoleucine degradation18/140448/84653.94e-043.06e-031.86e-0318
hsa006408ColorectumCRCPropanoate metabolism11/109132/84651.51e-031.17e-027.94e-0311
hsa006409ColorectumCRCPropanoate metabolism11/109132/84651.51e-031.17e-027.94e-0311
hsa002809EsophagusESCCValine, leucine and isoleucine degradation34/420548/84652.34e-036.54e-033.35e-0334
hsa0028014EsophagusESCCValine, leucine and isoleucine degradation34/420548/84652.34e-036.54e-033.35e-0334
hsa002806LiverNAFLDValine, leucine and isoleucine degradation20/104348/84653.03e-071.65e-051.33e-0520
hsa0064010LiverNAFLDPropanoate metabolism12/104332/84652.44e-044.45e-033.58e-0312
hsa0028011LiverNAFLDValine, leucine and isoleucine degradation20/104348/84653.03e-071.65e-051.33e-0520
hsa0064011LiverNAFLDPropanoate metabolism12/104332/84652.44e-044.45e-033.58e-0312
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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
BCKDHBSNVMissense_Mutationc.289G>Tp.Asp97Tyrp.D97YP21953protein_codingdeleterious(0)probably_damaging(1)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
BCKDHBinsertionNonsense_Mutationnovelc.1159_1160insCAAGCCCCTTCCTCATCTGCCCTGTAGGGCTGGGGAGGTGCTp.Arg387delinsProSerProPheLeuIleCysProValGlyLeuGlyArgCysTerp.R387delinsPSPFLICPVGLGRC*P21953protein_codingTCGA-AR-A0TY-01Breastbreast invasive carcinomaFemale<65I/IIUnspecificPaclitaxelPD
BCKDHBSNVMissense_Mutationrs779150907c.971N>Ap.Arg324Glnp.R324QP21953protein_codingdeleterious(0)probably_damaging(0.991)TCGA-AA-3812-01Colorectumcolon adenocarcinomaFemale>=65I/IIUnknownUnknownPD
BCKDHBSNVMissense_Mutationrs755159101c.1160N>Ap.Arg387Glnp.R387QP21953protein_codingtolerated(0.09)benign(0.012)TCGA-AZ-6605-01Colorectumcolon adenocarcinomaMale>=65III/IVChemotherapyfolfoxSD
BCKDHBSNVMissense_Mutationc.620G>Ap.Cys207Tyrp.C207YP21953protein_codingdeleterious(0.01)possibly_damaging(0.874)TCGA-CK-5913-01Colorectumcolon adenocarcinomaFemale<65I/IIUnknownUnknownSD
BCKDHBSNVMissense_Mutationrs398124561c.1016N>Tp.Ser339Leup.S339LP21953protein_codingdeleterious(0)possibly_damaging(0.526)TCGA-CM-4746-01Colorectumcolon adenocarcinomaMale<65I/IIUnknownUnknownSD
BCKDHBSNVMissense_Mutationc.790N>Ap.Glu264Lysp.E264KP21953protein_codingdeleterious(0.01)possibly_damaging(0.631)TCGA-EI-6917-01Colorectumrectum adenocarcinomaMale<65III/IVChemotherapy5fluorouracil+oxaciplatina+l-folinianSD
BCKDHBdeletionFrame_Shift_Delnovelc.199delCp.Gln67LysfsTer5p.Q67Kfs*5P21953protein_codingTCGA-F4-6805-01Colorectumcolon adenocarcinomaFemale<65I/IIChemotherapyxelodaCR
BCKDHBSNVMissense_Mutationnovelc.427G>Tp.Ala143Serp.A143SP21953protein_codingdeleterious(0.05)benign(0.321)TCGA-AJ-A2QO-01Endometriumuterine corpus endometrioid carcinomaFemale>=65I/IIUnknownUnknownSD
BCKDHBSNVMissense_Mutationnovelc.518A>Gp.Asp173Glyp.D173GP21953protein_codingtolerated(0.91)benign(0.005)TCGA-AJ-A3EL-01Endometriumuterine corpus endometrioid carcinomaFemale<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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