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: SMARCD1

Gene summary for SMARCD1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

SMARCD1

Gene ID

6602

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Gene AliasBAF60A
Cytomap12q13.12
Gene Typeprotein-coding
GO ID

GO:0006139

UniProtAcc

Q96GM5


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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
6602SMARCD1HTA11_411_2000001011HumanColorectumSER2.67e-024.72e-01-0.2602
6602SMARCD1HTA11_1391_2000001011HumanColorectumAD4.38e-052.32e-01-0.059
6602SMARCD1HTA11_2992_2000001011HumanColorectumSER1.77e-033.13e-01-0.1706
6602SMARCD1HTA11_866_3004761011HumanColorectumAD8.88e-052.28e-010.096
6602SMARCD1HTA11_99999965104_69814HumanColorectumMSS4.78e-032.54e-010.281
6602SMARCD1HTA11_99999971662_82457HumanColorectumMSS5.87e-175.44e-010.3859
6602SMARCD1HTA11_99999973899_84307HumanColorectumMSS1.45e-022.57e-010.2585
6602SMARCD1HTA11_99999974143_84620HumanColorectumMSS1.25e-022.50e-010.3005
6602SMARCD1LZE4THumanEsophagusESCC9.60e-031.43e-010.0811
6602SMARCD1LZE7THumanEsophagusESCC3.45e-063.45e-010.0667
6602SMARCD1LZE24THumanEsophagusESCC7.89e-123.34e-010.0596
6602SMARCD1P1T-EHumanEsophagusESCC3.90e-054.56e-010.0875
6602SMARCD1P2T-EHumanEsophagusESCC1.44e-459.14e-010.1177
6602SMARCD1P4T-EHumanEsophagusESCC5.21e-224.90e-010.1323
6602SMARCD1P5T-EHumanEsophagusESCC4.15e-081.55e-010.1327
6602SMARCD1P8T-EHumanEsophagusESCC9.72e-234.26e-010.0889
6602SMARCD1P9T-EHumanEsophagusESCC5.20e-041.58e-010.1131
6602SMARCD1P10T-EHumanEsophagusESCC1.32e-326.16e-010.116
6602SMARCD1P11T-EHumanEsophagusESCC2.65e-073.71e-010.1426
6602SMARCD1P12T-EHumanEsophagusESCC2.38e-234.15e-010.1122
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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
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:0022411ColorectumADcellular component disassembly147/3918443/187238.53e-106.76e-08147
GO:0032984ColorectumADprotein-containing complex disassembly81/3918224/187239.41e-084.65e-0681
GO:0006325ColorectumADchromatin organization119/3918409/187234.85e-058.33e-04119
GO:0032986ColorectumADprotein-DNA complex disassembly12/391820/187231.60e-042.21e-0312
GO:0031498ColorectumADchromatin disassembly11/391820/187238.39e-048.21e-0311
GO:0006337ColorectumADnucleosome disassembly10/391818/187231.31e-031.15e-0210
GO:0006354ColorectumADDNA-templated transcription, elongation31/391891/187232.46e-031.90e-0231
GO:0006368ColorectumADtranscription elongation from RNA polymerase II promoter24/391869/187235.35e-033.52e-0224
GO:0006338ColorectumADchromatin remodeling70/3918255/187237.44e-034.53e-0270
GO:00224111ColorectumSERcellular component disassembly114/2897443/187231.17e-089.59e-07114
GO:00329841ColorectumSERprotein-containing complex disassembly61/2897224/187234.17e-061.60e-0461
GO:00063251ColorectumSERchromatin organization89/2897409/187234.15e-046.17e-0389
GO:00314981ColorectumSERchromatin disassembly8/289720/187237.14e-034.99e-028
GO:00329861ColorectumSERprotein-DNA complex disassembly8/289720/187237.14e-034.99e-028
GO:00224112ColorectumMSScellular component disassembly130/3467443/187231.44e-088.46e-07130
GO:00329842ColorectumMSSprotein-containing complex disassembly69/3467224/187235.61e-061.50e-0469
GO:00329862ColorectumMSSprotein-DNA complex disassembly12/346720/187234.55e-058.35e-0412
GO:00063252ColorectumMSSchromatin organization107/3467409/187237.22e-051.21e-03107
GO:00314982ColorectumMSSchromatin disassembly11/346720/187232.77e-043.67e-0311
GO:00063371ColorectumMSSnucleosome disassembly10/346718/187234.76e-045.58e-0310
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05225ColorectumADHepatocellular carcinoma59/2092168/84651.50e-038.69e-035.54e-0359
hsa052251ColorectumADHepatocellular carcinoma59/2092168/84651.50e-038.69e-035.54e-0359
hsa047142ColorectumSERThermogenesis106/1580232/84651.15e-216.34e-204.61e-20106
hsa047143ColorectumSERThermogenesis106/1580232/84651.15e-216.34e-204.61e-20106
hsa047144ColorectumMSSThermogenesis113/1875232/84651.52e-194.62e-182.83e-18113
hsa052252ColorectumMSSHepatocellular carcinoma56/1875168/84655.04e-043.45e-032.11e-0356
hsa047145ColorectumMSSThermogenesis113/1875232/84651.52e-194.62e-182.83e-18113
hsa052253ColorectumMSSHepatocellular carcinoma56/1875168/84655.04e-043.45e-032.11e-0356
hsa04714211EsophagusESCCThermogenesis163/4205232/84659.22e-111.14e-095.86e-10163
hsa0522518EsophagusESCCHepatocellular carcinoma109/4205168/84654.27e-051.88e-049.64e-05109
hsa04714310EsophagusESCCThermogenesis163/4205232/84659.22e-111.14e-095.86e-10163
hsa0522519EsophagusESCCHepatocellular carcinoma109/4205168/84654.27e-051.88e-049.64e-05109
hsa0471422LiverHCCThermogenesis170/4020232/84655.36e-162.25e-141.25e-14170
hsa052258LiverHCCHepatocellular carcinoma106/4020168/84652.87e-051.85e-041.03e-04106
hsa0471432LiverHCCThermogenesis170/4020232/84655.36e-162.25e-141.25e-14170
hsa0522511LiverHCCHepatocellular carcinoma106/4020168/84652.87e-051.85e-041.03e-04106
hsa0471430Oral cavityOSCCThermogenesis138/3704232/84657.67e-074.35e-062.22e-06138
hsa0522516Oral cavityOSCCHepatocellular carcinoma97/3704168/84651.63e-045.52e-042.81e-0497
hsa04714113Oral cavityOSCCThermogenesis138/3704232/84657.67e-074.35e-062.22e-06138
hsa0522517Oral cavityOSCCHepatocellular carcinoma97/3704168/84651.63e-045.52e-042.81e-0497
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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
SMARCD1SNVMissense_Mutationnovelc.1177G>Ap.Asp393Asnp.D393NQ96GM5protein_codingdeleterious(0)possibly_damaging(0.552)TCGA-5L-AAT1-01Breastbreast invasive carcinomaFemale<65III/IVHormone TherapyletrozolSD
SMARCD1SNVMissense_Mutationc.526A>Gp.Ile176Valp.I176VQ96GM5protein_codingtolerated(0.4)benign(0.009)TCGA-E9-A1NH-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
SMARCD1SNVMissense_Mutationnovelc.463N>Tp.Arg155Trpp.R155WQ96GM5protein_codingdeleterious(0)probably_damaging(0.997)TCGA-E9-A6HE-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinCR
SMARCD1insertionIn_Frame_Insnovelc.1172_1173insCCGp.Asp391_Ile392insArgp.D391_I392insRQ96GM5protein_codingTCGA-A7-A0CJ-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
SMARCD1insertionNonsense_Mutationnovelc.1174_1175insCCTGGCCAAAAAAGTTTTAAAAATTATTATTATTATTTCTTTp.Ile392delinsThrTrpProLysLysPheTerLysLeuLeuLeuLeuPheLeuPhep.I392delinsTWPKKF*KLLLLFLFQ96GM5protein_codingTCGA-A7-A0CJ-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
SMARCD1insertionFrame_Shift_Insnovelc.1223_1224insTCAAp.Leu409GlnfsTer19p.L409Qfs*19Q96GM5protein_codingTCGA-BH-A0H9-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
SMARCD1insertionIn_Frame_Insnovelc.1344_1345insTGGp.Pro448_Gln449insTrpp.P448_Q449insWQ96GM5protein_codingTCGA-DS-A1OA-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycarboplatinPD
SMARCD1deletionIn_Frame_Delnovelc.1347_1349delNNNp.Gln449_Gly450delinsHisp.Q449_G450delinsHQ96GM5protein_codingTCGA-DS-A1OA-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycarboplatinPD
SMARCD1SNVMissense_Mutationnovelc.1312N>Tp.Arg438Trpp.R438WQ96GM5protein_codingdeleterious(0)probably_damaging(0.996)TCGA-5M-AAT6-01Colorectumcolon adenocarcinomaFemale<65III/IVUnknownUnknownPD
SMARCD1SNVMissense_Mutationc.1028T>Cp.Leu343Prop.L343PQ96GM5protein_codingdeleterious(0)probably_damaging(0.994)TCGA-AA-3672-01Colorectumcolon adenocarcinomaFemale>=65III/IVUnknownUnknownSD
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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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