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:2000116110Oral cavityLPregulation of cysteine-type endopeptidase activity109/4623235/187233.16e-132.91e-11109
GO:0043281110Oral cavityLPregulation of cysteine-type endopeptidase activity involved in apoptotic process99/4623209/187237.89e-136.68e-1199
GO:001050615Oral cavityLPregulation of autophagy132/4623317/187231.82e-111.28e-09132
GO:0009896110Oral cavityLPpositive regulation of catabolic process187/4623492/187232.30e-111.58e-09187
GO:0052547110Oral cavityLPregulation of peptidase activity177/4623461/187233.01e-112.00e-09177
GO:1904951110Oral cavityLPpositive regulation of establishment of protein localization132/4623319/187233.06e-112.00e-09132
GO:000700617Oral cavityLPmitochondrial membrane organization61/4623116/187239.44e-115.63e-0961
GO:005160416Oral cavityLPprotein maturation122/4623294/187231.37e-107.72e-09122
GO:0031331110Oral cavityLPpositive regulation of cellular catabolic process163/4623427/187233.03e-101.59e-08163
GO:0052548110Oral cavityLPregulation of endopeptidase activity164/4623432/187234.33e-102.20e-08164
GO:0051222110Oral cavityLPpositive regulation of protein transport123/4623303/187236.05e-102.96e-08123
GO:0010952110Oral cavityLPpositive regulation of peptidase activity88/4623197/187236.52e-103.14e-0888
GO:200123518Oral cavityLPpositive regulation of apoptotic signaling pathway63/4623126/187237.17e-103.43e-0863
GO:0000302110Oral cavityLPresponse to reactive oxygen species95/4623222/187232.23e-099.98e-0895
GO:0042542110Oral cavityLPresponse to hydrogen peroxide68/4623146/187236.95e-092.81e-0768
GO:000863019Oral cavityLPintrinsic apoptotic signaling pathway in response to DNA damage51/462399/187238.01e-093.20e-0751
GO:0062197110Oral cavityLPcellular response to chemical stress130/4623337/187238.94e-093.52e-07130
GO:0010950110Oral cavityLPpositive regulation of endopeptidase activity79/4623179/187239.34e-093.62e-0779
GO:0071496110Oral cavityLPcellular response to external stimulus124/4623320/187231.44e-085.36e-07124
GO:0097191110Oral cavityLPextrinsic apoptotic signaling pathway91/4623219/187232.69e-089.80e-0791
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0502020EndometriumAEHPrion disease110/1197273/84652.39e-272.44e-251.78e-25110
hsa0520826EndometriumAEHChemical carcinogenesis - reactive oxygen species91/1197223/84653.28e-231.33e-219.76e-2291
hsa0501420EndometriumAEHAmyotrophic lateral sclerosis123/1197364/84652.17e-227.82e-215.72e-21123
hsa0501020EndometriumAEHAlzheimer disease124/1197384/84651.20e-203.91e-192.86e-19124
hsa0502220EndometriumAEHPathways of neurodegeneration - multiple diseases137/1197476/84659.27e-182.32e-161.70e-16137
hsa0451015EndometriumAEHFocal adhesion58/1197203/84654.99e-087.37e-075.39e-0758
hsa0472216EndometriumAEHNeurotrophin signaling pathway31/1197119/84654.07e-043.07e-032.25e-0331
hsa0491920EndometriumAEHThyroid hormone signaling pathway30/1197121/84651.20e-037.52e-035.50e-0330
hsa0541726EndometriumAEHLipid and atherosclerosis47/1197215/84651.24e-037.62e-035.58e-0347
hsa052158EndometriumAEHProstate cancer25/119797/84651.68e-031.01e-027.39e-0325
hsa0421010EndometriumAEHApoptosis30/1197136/84657.72e-034.05e-022.96e-0230
hsa0517018EndometriumAEHHuman immunodeficiency virus 1 infection43/1197212/84658.19e-034.22e-023.09e-0243
hsa05020110EndometriumAEHPrion disease110/1197273/84652.39e-272.44e-251.78e-25110
hsa05208112EndometriumAEHChemical carcinogenesis - reactive oxygen species91/1197223/84653.28e-231.33e-219.76e-2291
hsa05014110EndometriumAEHAmyotrophic lateral sclerosis123/1197364/84652.17e-227.82e-215.72e-21123
hsa05010110EndometriumAEHAlzheimer disease124/1197384/84651.20e-203.91e-192.86e-19124
hsa05022110EndometriumAEHPathways of neurodegeneration - multiple diseases137/1197476/84659.27e-182.32e-161.70e-16137
hsa0451016EndometriumAEHFocal adhesion58/1197203/84654.99e-087.37e-075.39e-0758
hsa0472217EndometriumAEHNeurotrophin signaling pathway31/1197119/84654.07e-043.07e-032.25e-0331
hsa04919110EndometriumAEHThyroid hormone signaling pathway30/1197121/84651.20e-037.52e-035.50e-0330
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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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