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: HDAC9

Gene summary for HDAC9

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

HDAC9

Gene ID

9734

Gene namehistone deacetylase 9
Gene AliasHD7
Cytomap7p21.1
Gene Typeprotein-coding
GO ID

GO:0000122

UniProtAcc

Q9UKV0


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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
9734HDAC9HTA11_3410_2000001011HumanColorectumAD3.38e-042.29e-010.0155
9734HDAC9HTA11_2487_2000001011HumanColorectumSER2.27e-124.99e-01-0.1808
9734HDAC9HTA11_1938_2000001011HumanColorectumAD8.82e-157.51e-01-0.0811
9734HDAC9HTA11_78_2000001011HumanColorectumAD2.14e-054.95e-01-0.1088
9734HDAC9HTA11_347_2000001011HumanColorectumAD1.87e-287.28e-01-0.1954
9734HDAC9HTA11_411_2000001011HumanColorectumSER8.88e-119.95e-01-0.2602
9734HDAC9HTA11_2112_2000001011HumanColorectumSER2.88e-101.40e+00-0.2196
9734HDAC9HTA11_3361_2000001011HumanColorectumAD1.29e-125.76e-01-0.1207
9734HDAC9HTA11_83_2000001011HumanColorectumSER1.97e-063.69e-01-0.1526
9734HDAC9HTA11_696_2000001011HumanColorectumAD9.88e-216.28e-01-0.1464
9734HDAC9HTA11_866_2000001011HumanColorectumAD1.53e-043.47e-01-0.1001
9734HDAC9HTA11_1391_2000001011HumanColorectumAD1.98e-115.66e-01-0.059
9734HDAC9HTA11_2992_2000001011HumanColorectumSER9.46e-033.27e-01-0.1706
9734HDAC9HTA11_5216_2000001011HumanColorectumSER4.34e-023.45e-01-0.1462
9734HDAC9HTA11_9341_2000001011HumanColorectumSER1.04e-034.74e-01-0.00410000000000005
9734HDAC9HTA11_7862_2000001011HumanColorectumAD1.49e-024.02e-01-0.0179
9734HDAC9HTA11_10623_2000001011HumanColorectumAD2.65e-129.15e-01-0.0177
9734HDAC9HTA11_7696_3000711011HumanColorectumAD2.51e-145.43e-010.0674
9734HDAC9HTA11_6818_2000001011HumanColorectumAD7.49e-271.63e+000.0112
9734HDAC9HTA11_11156_2000001011HumanColorectumAD1.25e-121.39e+000.0397
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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
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
GCThe 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.CAG: Chronic atrophic gastritis
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
CSG: Chronic superficial gastritis
GC: Gastric cancer
SIM: Severe intestinal metaplasia
WIM: Wild intestinal metaplasia
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
∗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:001063223Oral cavityNEOLPregulation of epithelial cell migration56/2005292/187231.07e-051.98e-0456
GO:001470621Oral cavityNEOLPstriated muscle tissue development69/2005384/187231.11e-052.06e-0469
GO:003009821Oral cavityNEOLPlymphocyte differentiation66/2005374/187233.08e-054.67e-0466
GO:003286832Oral cavityNEOLPresponse to insulin50/2005264/187234.35e-056.13e-0450
GO:001063424Oral cavityNEOLPpositive regulation of epithelial cell migration37/2005176/187234.37e-056.14e-0437
GO:001820531Oral cavityNEOLPpeptidyl-lysine modification64/2005376/187231.21e-041.43e-0364
GO:005114615Oral cavityNEOLPstriated muscle cell differentiation51/2005283/187231.37e-041.60e-0351
GO:000751714Oral cavityNEOLPmuscle organ development56/2005327/187232.65e-042.70e-0356
GO:001059514Oral cavityNEOLPpositive regulation of endothelial cell migration28/2005133/187233.44e-043.33e-0328
GO:006053813Oral cavityNEOLPskeletal muscle organ development32/2005166/187237.05e-045.81e-0332
GO:004353613Oral cavityNEOLPpositive regulation of blood vessel endothelial cell migration18/200576/187239.09e-047.10e-0318
GO:001059414Oral cavityNEOLPregulation of endothelial cell migration40/2005232/187231.64e-031.14e-0240
GO:004353413Oral cavityNEOLPblood vessel endothelial cell migration32/2005176/187231.93e-031.30e-0232
GO:000751912Oral cavityNEOLPskeletal muscle tissue development29/2005155/187231.97e-031.32e-0229
GO:000647631Oral cavityNEOLPprotein deacetylation21/2005101/187232.11e-031.39e-0221
GO:005500111Oral cavityNEOLPmuscle cell development32/2005184/187233.95e-032.26e-0232
GO:0002040Oral cavityNEOLPsprouting angiogenesis32/2005185/187234.29e-032.42e-0232
GO:000197512Oral cavityNEOLPresponse to amphetamine9/200533/187236.45e-033.32e-029
GO:003560131Oral cavityNEOLPprotein deacylation21/2005112/187237.48e-033.74e-0221
GO:0030183Oral cavityNEOLPB cell differentiation25/2005141/187237.85e-033.90e-0225
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa0520325EsophagusESCCViral carcinogenesis137/4205204/84652.47e-071.88e-069.62e-07137
hsa0520335EsophagusESCCViral carcinogenesis137/4205204/84652.47e-071.88e-069.62e-07137
hsa052034LungIACViral carcinogenesis43/1053204/84653.02e-043.07e-032.04e-0343
hsa0520311LungIACViral carcinogenesis43/1053204/84653.02e-043.07e-032.04e-0343
hsa052038Oral cavityOSCCViral carcinogenesis124/3704204/84655.57e-073.28e-061.67e-06124
hsa0520314Oral cavityOSCCViral carcinogenesis124/3704204/84655.57e-073.28e-061.67e-06124
hsa0520342Oral cavityEOLPViral carcinogenesis55/1218204/84651.54e-061.34e-057.92e-0655
hsa0520351Oral cavityEOLPViral carcinogenesis55/1218204/84651.54e-061.34e-057.92e-0655
hsa0520361Oral cavityNEOLPViral carcinogenesis56/1112204/84652.90e-085.34e-073.36e-0756
hsa0520371Oral cavityNEOLPViral carcinogenesis56/1112204/84652.90e-085.34e-073.36e-0756
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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
HDAC9SNVMissense_Mutationc.3178N>Ap.Gly1060Serp.G1060SQ9UKV0protein_codingtolerated(0.21)benign(0.168)TCGA-A2-A0D2-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinSD
HDAC9SNVMissense_Mutationc.2057N>Tp.Arg686Leup.R686LQ9UKV0protein_codingdeleterious(0.01)probably_damaging(0.992)TCGA-A2-A0SV-01Breastbreast invasive carcinomaFemale<65III/IVOther, specify in notesBisphosphonate therapyzometaPD
HDAC9SNVMissense_Mutationc.1846N>Tp.Pro616Serp.P616SQ9UKV0protein_codingdeleterious(0.01)possibly_damaging(0.696)TCGA-AR-A251-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapydoxorubicinSD
HDAC9SNVMissense_Mutationc.407G>Cp.Gly136Alap.G136AQ9UKV0protein_codingdeleterious(0.04)benign(0.164)TCGA-BH-A0B7-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapyadriamycinCR
HDAC9SNVMissense_Mutationnovelc.2986N>Tp.Ala996Serp.A996SQ9UKV0protein_codingdeleterious(0.01)probably_damaging(0.988)TCGA-E2-A15M-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapyarimidexSD
HDAC9SNVMissense_Mutationc.2093C>Tp.Ser698Phep.S698FQ9UKV0protein_codingdeleterious(0.01)possibly_damaging(0.852)TCGA-DR-A0ZM-01Cervixcervical & endocervical cancerFemale<65III/IVUnspecificCisplatinSD
HDAC9SNVMissense_Mutationc.839N>Tp.Ser280Leup.S280LQ9UKV0protein_codingtolerated(0.08)probably_damaging(0.994)TCGA-EK-A2PG-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
HDAC9SNVMissense_Mutationc.1096N>Tp.Pro366Serp.P366SQ9UKV0protein_codingtolerated(0.33)benign(0)TCGA-FU-A23L-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
HDAC9SNVMissense_Mutationc.702A>Cp.Lys234Asnp.K234NQ9UKV0protein_codingdeleterious(0)probably_damaging(0.997)TCGA-FU-A3HZ-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
HDAC9SNVMissense_Mutationnovelc.2773C>Tp.Pro925Serp.P925SQ9UKV0protein_codingtolerated(0.07)possibly_damaging(0.692)TCGA-VS-A94Z-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinCR
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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
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEinhibitorSB939
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEinhibitorPCI-24781ABEXINOSTAT
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEinhibitor310264675CUDC-101
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEMOCETINOSTATMOCETINOSTAT23829483,26287310
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEBUTYRYLHYDROXAMIC ACIDBUTYRYLHYDROXAMIC ACID21874153
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEinhibitorROMIDEPSINROMIDEPSIN
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEPMID29671355-Compound-25
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMESUBEROHYDROXAMIC ACIDSUBEROHYDROXAMIC ACID16921367
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEinhibitorCUDC-101CUDC-101
9734HDAC9TRANSCRIPTION FACTOR BINDING, TRANSCRIPTION FACTOR COMPLEX, ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOMEVORINOSTATVORINOSTAT
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