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: PSMD9

Gene summary for PSMD9

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PSMD9

Gene ID

5715

Gene nameproteasome 26S subunit, non-ATPase 9
Gene AliasRpn4
Cytomap12q24.31
Gene Typeprotein-coding
GO ID

GO:0002790

UniProtAcc

O00233


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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
5715PSMD9HTA11_1938_2000001011HumanColorectumAD4.00e-031.63e-01-0.0811
5715PSMD9HTA11_78_2000001011HumanColorectumAD4.96e-029.84e-02-0.1088
5715PSMD9HTA11_347_2000001011HumanColorectumAD2.84e-081.87e-01-0.1954
5715PSMD9HTA11_83_2000001011HumanColorectumSER2.92e-072.45e-01-0.1526
5715PSMD9HTA11_696_2000001011HumanColorectumAD1.96e-102.09e-01-0.1464
5715PSMD9HTA11_866_2000001011HumanColorectumAD8.62e-041.02e-01-0.1001
5715PSMD9HTA11_1391_2000001011HumanColorectumAD5.72e-123.03e-01-0.059
5715PSMD9HTA11_7862_2000001011HumanColorectumAD1.24e-021.98e-01-0.0179
5715PSMD9HTA11_866_3004761011HumanColorectumAD3.01e-092.28e-010.096
5715PSMD9HTA11_4255_2000001011HumanColorectumSER3.40e-022.22e-010.0446
5715PSMD9HTA11_10711_2000001011HumanColorectumAD4.64e-041.83e-010.0338
5715PSMD9HTA11_7696_3000711011HumanColorectumAD4.46e-071.52e-010.0674
5715PSMD9HTA11_6818_2000001011HumanColorectumAD1.38e-073.43e-010.0112
5715PSMD9HTA11_6818_2000001021HumanColorectumAD5.94e-143.55e-010.0588
5715PSMD9HTA11_99999970781_79442HumanColorectumMSS2.00e-051.25e-010.294
5715PSMD9HTA11_99999965062_69753HumanColorectumMSI-H7.89e-033.22e-010.3487
5715PSMD9HTA11_99999971662_82457HumanColorectumMSS7.11e-143.05e-010.3859
5715PSMD9HTA11_99999973899_84307HumanColorectumMSS1.46e-021.84e-010.2585
5715PSMD9HTA11_99999974143_84620HumanColorectumMSS9.63e-081.82e-010.3005
5715PSMD9LZE3DHumanEsophagusHGIN6.56e-038.76e-010.0668
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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:00320242ColorectumMSI-Hpositive regulation of insulin secretion13/131978/187232.98e-033.78e-0213
GO:190495120EsophagusHGINpositive regulation of establishment of protein localization73/2587319/187236.99e-062.14e-0473
GO:005122220EsophagusHGINpositive regulation of protein transport67/2587303/187235.13e-051.22e-0367
GO:00432483EsophagusHGINproteasome assembly6/258712/187233.03e-032.88e-026
GO:1904951111EsophagusESCCpositive regulation of establishment of protein localization216/8552319/187231.01e-156.86e-14216
GO:0051222111EsophagusESCCpositive regulation of protein transport204/8552303/187231.56e-148.38e-13204
GO:004324811EsophagusESCCproteasome assembly11/855212/187231.26e-036.06e-0311
GO:00512244EsophagusESCCnegative regulation of protein transport74/8552127/187232.86e-031.21e-0274
GO:19049505EsophagusESCCnegative regulation of establishment of protein localization76/8552131/187232.96e-031.24e-0276
GO:000930617EsophagusESCCprotein secretion190/8552359/187233.22e-031.34e-02190
GO:003559217EsophagusESCCestablishment of protein localization to extracellular region190/8552360/187233.77e-031.53e-02190
GO:007169210EsophagusESCCprotein localization to extracellular region193/8552368/187235.01e-031.92e-02193
GO:005070810EsophagusESCCregulation of protein secretion142/8552268/187239.31e-033.24e-02142
GO:005071416EsophagusESCCpositive regulation of protein secretion76/8552137/187231.32e-024.31e-0276
GO:190495112LiverCirrhoticpositive regulation of establishment of protein localization135/4634319/187233.20e-122.28e-10135
GO:005122212LiverCirrhoticpositive regulation of protein transport126/4634303/187236.85e-113.77e-09126
GO:0043248LiverCirrhoticproteasome assembly9/463412/187233.59e-043.03e-039
GO:19049502LiverCirrhoticnegative regulation of establishment of protein localization49/4634131/187238.50e-046.15e-0349
GO:0051224LiverCirrhoticnegative regulation of protein transport47/4634127/187231.39e-039.27e-0347
GO:00510514LiverCirrhoticnegative regulation of transport141/4634470/187235.06e-032.62e-02141
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check button Enriched KEGG pathways.
Pathway IDTissueDisease StageDescriptionGene RatioBg Ratiopvaluep.adjustqvalueCount
hsa05012ColorectumADParkinson disease147/2092266/84652.53e-278.48e-255.41e-25147
hsa05010ColorectumADAlzheimer disease174/2092384/84651.82e-199.26e-185.91e-18174
hsa05016ColorectumADHuntington disease147/2092306/84651.93e-199.26e-185.91e-18147
hsa05020ColorectumADPrion disease133/2092273/84652.47e-188.29e-175.29e-17133
hsa05014ColorectumADAmyotrophic lateral sclerosis164/2092364/84654.28e-181.27e-168.09e-17164
hsa05022ColorectumADPathways of neurodegeneration - multiple diseases201/2092476/84654.54e-181.27e-168.09e-17201
hsa03050ColorectumADProteasome29/209246/84653.87e-086.18e-073.94e-0729
hsa05017ColorectumADSpinocerebellar ataxia60/2092143/84653.78e-064.35e-052.78e-0560
hsa050121ColorectumADParkinson disease147/2092266/84652.53e-278.48e-255.41e-25147
hsa050101ColorectumADAlzheimer disease174/2092384/84651.82e-199.26e-185.91e-18174
hsa050161ColorectumADHuntington disease147/2092306/84651.93e-199.26e-185.91e-18147
hsa050201ColorectumADPrion disease133/2092273/84652.47e-188.29e-175.29e-17133
hsa050141ColorectumADAmyotrophic lateral sclerosis164/2092364/84654.28e-181.27e-168.09e-17164
hsa050221ColorectumADPathways of neurodegeneration - multiple diseases201/2092476/84654.54e-181.27e-168.09e-17201
hsa030501ColorectumADProteasome29/209246/84653.87e-086.18e-073.94e-0729
hsa050171ColorectumADSpinocerebellar ataxia60/2092143/84653.78e-064.35e-052.78e-0560
hsa050122ColorectumSERParkinson disease132/1580266/84652.72e-319.03e-296.55e-29132
hsa050202ColorectumSERPrion disease119/1580273/84654.61e-223.06e-202.22e-20119
hsa050162ColorectumSERHuntington disease127/1580306/84653.29e-211.37e-199.92e-20127
hsa050102ColorectumSERAlzheimer disease146/1580384/84656.52e-202.40e-181.75e-18146
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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
PSMD9SNVMissense_Mutationnovelc.586G>Tp.Gly196Trpp.G196WO00233protein_codingdeleterious(0)probably_damaging(0.998)TCGA-BH-A1EN-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PSMD9SNVMissense_Mutationc.20G>Ap.Arg7Lysp.R7KO00233protein_codingtolerated_low_confidence(0.94)benign(0)TCGA-D8-A13Z-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapydoxorubicineSD
PSMD9SNVMissense_Mutationrs778204603c.581G>Tp.Arg194Leup.R194LO00233protein_codingdeleterious(0)probably_damaging(0.991)TCGA-C5-A2LT-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapycisplatinSD
PSMD9SNVMissense_Mutationnovelc.136N>Cp.Ser46Argp.S46RO00233protein_codingtolerated(0.1)benign(0.027)TCGA-DS-A1OC-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapygemcitabineSD
PSMD9SNVMissense_Mutationnovelc.137N>Ap.Ser46Asnp.S46NO00233protein_codingtolerated(0.17)benign(0.147)TCGA-DS-A1OC-01Cervixcervical & endocervical cancerFemale<65I/IIChemotherapygemcitabineSD
PSMD9SNVMissense_Mutationc.73N>Cp.Glu25Glnp.E25QO00233protein_codingtolerated(0.6)benign(0.003)TCGA-EK-A2PG-01Cervixcervical & endocervical cancerFemale>=65I/IIUnknownUnknownSD
PSMD9SNVMissense_Mutationc.472N>Ap.Glu158Lysp.E158KO00233protein_codingtolerated(0.19)possibly_damaging(0.56)TCGA-IR-A3LK-01Cervixcervical & endocervical cancerFemale>=65I/IIChemotherapycisplatinPD
PSMD9SNVMissense_Mutationrs758694222c.580N>Tp.Arg194Cysp.R194CO00233protein_codingdeleterious(0)probably_damaging(0.998)TCGA-AA-A010-01Colorectumcolon adenocarcinomaFemale<65I/IIChemotherapyfolinicCR
PSMD9SNVMissense_Mutationnovelc.299T>Ap.Leu100Glnp.L100QO00233protein_codingdeleterious(0)probably_damaging(0.979)TCGA-AG-A00Y-01Colorectumrectum adenocarcinomaMale>=65I/IIUnknownUnknownPD
PSMD9SNVMissense_Mutationnovelc.659C>Ap.Pro220Hisp.P220HO00233protein_codingdeleterious(0)probably_damaging(0.975)TCGA-A5-A0G2-01Endometriumuterine corpus endometrioid carcinomaFemale<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
5715PSMD9NAinhibitorBORTEZOMIBBORTEZOMIB
5715PSMD9NAinhibitorCARFILZOMIBCARFILZOMIB
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