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: BAD

Gene summary for BAD

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

BAD

Gene ID

572

Gene nameBCL2 associated agonist of cell death
Gene AliasBBC2
Cytomap11q13.1
Gene Typeprotein-coding
GO ID

GO:0000003

UniProtAcc

A0A024R562


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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
572BADAEH-subject1HumanEndometriumAEH1.11e-12-2.60e-01-0.3059
572BADAEH-subject2HumanEndometriumAEH1.95e-06-2.58e-01-0.2525
572BADAEH-subject3HumanEndometriumAEH4.47e-07-1.68e-01-0.2576
572BADAEH-subject4HumanEndometriumAEH1.47e-06-2.53e-01-0.2657
572BADAEH-subject5HumanEndometriumAEH7.79e-14-3.91e-01-0.2953
572BADEEC-subject1HumanEndometriumEEC9.41e-18-3.33e-01-0.2682
572BADEEC-subject2HumanEndometriumEEC2.85e-06-2.21e-01-0.2607
572BADEEC-subject3HumanEndometriumEEC3.83e-39-4.12e-01-0.2525
572BADEEC-subject4HumanEndometriumEEC1.48e-06-2.43e-01-0.2571
572BADEEC-subject5HumanEndometriumEEC1.26e-03-2.44e-01-0.249
572BADGSM5276934HumanEndometriumEEC1.54e-17-3.89e-01-0.0913
572BADGSM5276937HumanEndometriumEEC1.66e-10-3.71e-01-0.0897
572BADGSM6177620_NYU_UCEC1_lib1_lib1HumanEndometriumEEC1.48e-25-4.68e-01-0.1869
572BADGSM6177620_NYU_UCEC1_lib2_lib2HumanEndometriumEEC1.12e-26-4.48e-01-0.1875
572BADGSM6177620_NYU_UCEC1_lib3_lib3HumanEndometriumEEC3.24e-30-4.48e-01-0.1883
572BADGSM6177621_NYU_UCEC2_lib1_lib1HumanEndometriumEEC3.56e-32-4.31e-01-0.1934
572BADGSM6177622_NYU_UCEC3_lib1_lib1HumanEndometriumEEC8.26e-43-4.73e-01-0.1917
572BADGSM6177622_NYU_UCEC3_lib2_lib2HumanEndometriumEEC3.92e-31-4.54e-01-0.1916
572BADGSM6177623_NYU_UCEC3_VisHumanEndometriumEEC5.00e-08-1.52e-01-0.1269
572BADLZE4THumanEsophagusESCC1.76e-216.87e-010.0811
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
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:0044282ColorectumADsmall molecule catabolic process118/3918376/187231.05e-063.55e-05118
GO:0009083ColorectumADbranched-chain amino acid catabolic process10/391815/187231.68e-042.29e-0310
GO:0016054ColorectumADorganic acid catabolic process73/3918240/187233.20e-043.81e-0373
GO:0046395ColorectumADcarboxylic acid catabolic process70/3918236/187239.06e-048.71e-0370
GO:0006520ColorectumADcellular amino acid metabolic process81/3918284/187231.37e-031.19e-0281
GO:0009081ColorectumADbranched-chain amino acid metabolic process10/391819/187232.25e-031.77e-0210
GO:00090831ColorectumMSSbranched-chain amino acid catabolic process10/346715/187235.64e-059.87e-0410
GO:00090811ColorectumMSSbranched-chain amino acid metabolic process10/346719/187238.39e-048.68e-0310
GO:00442822ColorectumMSSsmall molecule catabolic process94/3467376/187239.85e-049.86e-0394
GO:00160542ColorectumMSSorganic acid catabolic process61/3467240/187234.72e-033.31e-0261
GO:00442823ColorectumFAPsmall molecule catabolic process77/2622376/187233.25e-044.16e-0377
GO:00160543ColorectumFAPorganic acid catabolic process50/2622240/187232.30e-031.85e-0250
GO:00090832ColorectumFAPbranched-chain amino acid catabolic process7/262215/187232.40e-031.90e-027
GO:00463951ColorectumFAPcarboxylic acid catabolic process48/2622236/187234.53e-033.08e-0248
GO:00090833ColorectumCRCbranched-chain amino acid catabolic process6/207815/187233.82e-033.19e-026
GO:004603416EndometriumAEHATP metabolic process106/2100277/187234.13e-321.24e-28106
GO:009719316EndometriumAEHintrinsic apoptotic signaling pathway75/2100288/187231.46e-122.83e-1075
GO:200123316EndometriumAEHregulation of apoptotic signaling pathway86/2100356/187232.97e-124.95e-1086
GO:000683910EndometriumAEHmitochondrial transport66/2100254/187233.55e-114.96e-0966
GO:004578516EndometriumAEHpositive regulation of cell adhesion96/2100437/187235.50e-117.18e-0996
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa015243LiverHCCPlatinum drug resistance52/402073/84653.14e-051.88e-041.04e-0452
hsa051653LiverHCCHuman papillomavirus infection188/4020331/84653.34e-041.49e-038.29e-04188
hsa0517012LiverHCCHuman immunodeficiency virus 1 infection125/4020212/84654.51e-041.94e-031.08e-03125
hsa0472211LiverHCCNeurotrophin signaling pathway74/4020119/84658.27e-043.26e-031.81e-0374
hsa0491913LiverHCCThyroid hormone signaling pathway75/4020121/84658.76e-043.38e-031.88e-0375
hsa0514531LiverHCCToxoplasmosis70/4020112/84659.25e-043.52e-031.96e-0370
hsa042103LiverHCCApoptosis83/4020136/84659.51e-043.58e-031.99e-0383
hsa0516031LiverHCCHepatitis C94/4020157/84651.11e-034.10e-032.28e-0394
hsa0401211LiverHCCErbB signaling pathway54/402085/84652.02e-037.07e-033.93e-0354
hsa052033LiverHCCViral carcinogenesis117/4020204/84652.68e-038.98e-035.00e-03117
hsa0522311LiverHCCNon-small cell lung cancer46/402072/84653.61e-031.12e-026.22e-0346
hsa0152131LiverHCCEGFR tyrosine kinase inhibitor resistance48/402079/84651.19e-022.99e-021.66e-0248
hsa015221LiverHCCEndocrine resistance58/402098/84651.28e-023.19e-021.78e-0258
hsa0516111LiverHCCHepatitis B91/4020162/84651.56e-023.76e-022.09e-0291
hsa052211LiverHCCAcute myeloid leukemia41/402067/84651.64e-023.90e-022.17e-0241
hsa0541752LiverHCCLipid and atherosclerosis118/4020215/84651.66e-023.92e-022.18e-02118
hsa0501428Oral cavityOSCCAmyotrophic lateral sclerosis246/3704364/84656.65e-211.11e-185.67e-19246
hsa0501028Oral cavityOSCCAlzheimer disease244/3704384/84651.18e-153.60e-141.83e-14244
hsa0502228Oral cavityOSCCPathways of neurodegeneration - multiple diseases292/3704476/84651.60e-154.47e-142.28e-14292
hsa0502028Oral cavityOSCCPrion disease181/3704273/84652.05e-145.30e-132.70e-13181
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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
BADMYOFIBEsophagusADJFIBCD1,SLC22A23,S100A3, etc.0.00e+00The 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.
BADINCAFEsophagusADJFIBCD1,SLC22A23,S100A3, etc.0.00e+00The 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.
BADSMCEsophagusESCCFIBCD1,SLC22A23,S100A3, etc.5.49e-03The 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.
BADFIBEsophagusESCCFIBCD1,SLC22A23,S100A3, etc.0.00e+00The 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.
∗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
BADSNVMissense_Mutationc.351G>Ap.Met117Ilep.M117IQ92934protein_codingdeleterious(0)probably_damaging(0.966)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
BADSNVMissense_Mutationc.293N>Ap.Arg98Hisp.R98HQ92934protein_codingdeleterious(0.03)possibly_damaging(0.688)TCGA-EK-A2RK-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
BADSNVMissense_Mutationc.57G>Cp.Glu19Aspp.E19DQ92934protein_codingtolerated_low_confidence(1)benign(0.001)TCGA-4N-A93T-01Colorectumcolon adenocarcinomaMale>=65III/IVChemotherapyxelodaSD
BADSNVMissense_Mutationrs775688969c.74N>Ap.Ser25Asnp.S25NQ92934protein_codingtolerated(0.13)benign(0.409)TCGA-AA-A010-01Colorectumcolon adenocarcinomaFemale<65I/IIChemotherapyfolinicCR
BADSNVMissense_Mutationnovelc.212G>Tp.Ser71Ilep.S71IQ92934protein_codingdeleterious(0.01)possibly_damaging(0.857)TCGA-AJ-A5DW-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
BADSNVMissense_Mutationnovelc.401N>Tp.Ser134Ilep.S134IQ92934protein_codingdeleterious(0)probably_damaging(0.998)TCGA-AX-A1CE-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnspecificPaclitaxelSD
BADSNVMissense_Mutationnovelc.485N>Ap.Gly162Glup.G162EQ92934protein_codingdeleterious_low_confidence(0)probably_damaging(1)TCGA-AX-A2HC-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapypaclitaxelPD
BADSNVMissense_Mutationc.298N>Ap.Ala100Thrp.A100TQ92934protein_codingdeleterious(0)probably_damaging(0.999)TCGA-D1-A17R-01Endometriumuterine corpus endometrioid carcinomaFemale<65I/IIUnknownUnknownSD
BADSNVMissense_Mutationc.128G>Ap.Gly43Aspp.G43DQ92934protein_codingtolerated(0.08)probably_damaging(1)TCGA-FI-A2D5-01Endometriumuterine corpus endometrioid carcinomaFemale<65III/IVChemotherapycarboplatinumPD
BADSNVMissense_Mutationc.483N>Tp.Arg161Serp.R161SQ92934protein_codingdeleterious_low_confidence(0)benign(0.272)TCGA-CH-5739-01Prostateprostate adenocarcinomaMale>=657UnknownUnknownSD
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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
572BADKINASE, DRUGGABLE GENOMERUBOXISTAURINRUBOXISTAURIN18077363
572BADKINASE, DRUGGABLE GENOMEAT-101ISOSORBIDE
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