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: BRWD1

Gene summary for BRWD1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

BRWD1

Gene ID

54014

Gene namebromodomain and WD repeat domain containing 1
Gene AliasC21orf107
Cytomap21q22.2
Gene Typeprotein-coding
GO ID

GO:0000902

UniProtAcc

Q9NSI6


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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
54014BRWD1CA_HPV_1HumanCervixCC2.64e-02-7.70e-020.0264
54014BRWD1CCI_1HumanCervixCC2.95e-036.92e-010.528
54014BRWD1CCI_2HumanCervixCC3.70e-051.05e+000.5249
54014BRWD1CCI_3HumanCervixCC5.42e-101.00e+000.516
54014BRWD1sample3HumanCervixCC6.78e-031.09e-010.1387
54014BRWD1HTA11_3410_2000001011HumanColorectumAD5.64e-30-8.05e-010.0155
54014BRWD1HTA11_2487_2000001011HumanColorectumSER3.75e-12-6.19e-01-0.1808
54014BRWD1HTA11_2951_2000001011HumanColorectumAD4.17e-05-8.09e-010.0216
54014BRWD1HTA11_3361_2000001011HumanColorectumAD4.06e-09-7.29e-01-0.1207
54014BRWD1HTA11_83_2000001011HumanColorectumSER9.04e-06-6.01e-01-0.1526
54014BRWD1HTA11_696_2000001011HumanColorectumAD4.77e-13-4.59e-01-0.1464
54014BRWD1HTA11_866_2000001011HumanColorectumAD9.56e-08-3.94e-01-0.1001
54014BRWD1HTA11_1391_2000001011HumanColorectumAD9.37e-11-6.16e-01-0.059
54014BRWD1HTA11_5212_2000001011HumanColorectumAD6.21e-04-7.46e-01-0.2061
54014BRWD1HTA11_5216_2000001011HumanColorectumSER8.54e-03-7.81e-01-0.1462
54014BRWD1HTA11_546_2000001011HumanColorectumAD6.03e-08-7.56e-01-0.0842
54014BRWD1HTA11_7862_2000001011HumanColorectumAD3.14e-02-5.04e-01-0.0179
54014BRWD1HTA11_866_3004761011HumanColorectumAD4.74e-12-5.93e-010.096
54014BRWD1HTA11_8622_2000001021HumanColorectumSER3.53e-06-7.05e-010.0528
54014BRWD1HTA11_10711_2000001011HumanColorectumAD1.94e-04-4.51e-010.0338
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check button Transcriptomic changes along malignancy continuum.
TissueExpression DynamicsAbbreviation
CervixThe 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.CC: Cervix cancer
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
N_HPV: HPV-infected normal cervix
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
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:002260410CervixCCregulation of cell morphogenesis84/2311309/187231.00e-124.29e-1084
GO:00083608CervixCCregulation of cell shape38/2311154/187231.86e-053.46e-0438
GO:0022604ColorectumADregulation of cell morphogenesis109/3918309/187233.08e-092.07e-07109
GO:0008360ColorectumADregulation of cell shape56/3918154/187237.01e-061.73e-0456
GO:00226041ColorectumSERregulation of cell morphogenesis89/2897309/187231.51e-091.52e-0789
GO:00083601ColorectumSERregulation of cell shape43/2897154/187235.47e-051.30e-0343
GO:00226042ColorectumMSSregulation of cell morphogenesis103/3467309/187232.70e-102.56e-08103
GO:00083602ColorectumMSSregulation of cell shape52/3467154/187234.40e-061.24e-0452
GO:00226044ColorectumFAPregulation of cell morphogenesis87/2622309/187234.89e-111.87e-0887
GO:00083603ColorectumFAPregulation of cell shape43/2622154/187234.55e-061.52e-0443
GO:00226045ColorectumCRCregulation of cell morphogenesis74/2078309/187239.25e-115.04e-0874
GO:00083604ColorectumCRCregulation of cell shape38/2078154/187231.51e-068.15e-0538
GO:002260420EsophagusESCCregulation of cell morphogenesis180/8552309/187235.19e-065.45e-05180
GO:000836018EsophagusESCCregulation of cell shape92/8552154/187233.00e-041.81e-0392
GO:00226047LiverNAFLDregulation of cell morphogenesis62/1882309/187238.35e-087.09e-0662
GO:00083606LiverNAFLDregulation of cell shape27/1882154/187232.92e-032.65e-0227
GO:002260412LiverCirrhoticregulation of cell morphogenesis127/4634309/187231.45e-107.44e-09127
GO:000836012LiverCirrhoticregulation of cell shape69/4634154/187234.21e-081.36e-0669
GO:002260422LiverHCCregulation of cell morphogenesis188/7958309/187234.84e-111.82e-09188
GO:000836022LiverHCCregulation of cell shape92/7958154/187231.15e-051.31e-0492
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
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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
BRWD1SNVMissense_Mutationc.4784G>Cp.Arg1595Thrp.R1595TQ9NSI6protein_codingtolerated(0.05)benign(0.096)TCGA-A2-A0CW-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyanastrozoleSD
BRWD1SNVMissense_Mutationnovelc.3551N>Gp.Ala1184Glyp.A1184GQ9NSI6protein_codingtolerated(0.1)probably_damaging(0.926)TCGA-A2-A3Y0-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinCR
BRWD1SNVMissense_Mutationc.5956N>Cp.Glu1986Glnp.E1986QQ9NSI6protein_codingdeleterious_low_confidence(0.05)benign(0.23)TCGA-A8-A09M-01Breastbreast invasive carcinomaFemale>=65III/IVChemotherapypaclitaxelCR
BRWD1SNVMissense_Mutationc.3436G>Cp.Glu1146Glnp.E1146QQ9NSI6protein_codingtolerated(0.21)possibly_damaging(0.63)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
BRWD1SNVMissense_Mutationnovelc.2423N>Tp.Arg808Ilep.R808IQ9NSI6protein_codingdeleterious(0.01)possibly_damaging(0.548)TCGA-AN-A046-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
BRWD1SNVMissense_Mutationc.3668N>Gp.Ser1223Cysp.S1223CQ9NSI6protein_codingdeleterious(0)probably_damaging(1)TCGA-AN-A0XR-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
BRWD1SNVMissense_Mutationnovelc.614N>Tp.Ser205Leup.S205LQ9NSI6protein_codingdeleterious(0)probably_damaging(0.971)TCGA-AR-A2LE-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenPD
BRWD1SNVMissense_Mutationc.4949N>Gp.Ser1650Cysp.S1650CQ9NSI6protein_codingtolerated(0.1)possibly_damaging(0.87)TCGA-BH-A0DZ-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydocetaxelSD
BRWD1SNVMissense_Mutationc.5464N>Gp.Ser1822Alap.S1822AQ9NSI6protein_codingtolerated_low_confidence(0.61)possibly_damaging(0.446)TCGA-C8-A12W-01Breastbreast invasive carcinomaFemale<65III/IVUnknownUnknownSD
BRWD1SNVMissense_Mutationc.773N>Tp.Arg258Ilep.R258IQ9NSI6protein_codingdeleterious(0)probably_damaging(0.963)TCGA-D8-A1JK-01Breastbreast invasive 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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