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: PSMD1

Gene summary for PSMD1

check button Gene summary.

Gene informationSpeciesHuman
Gene symbol

PSMD1

Gene ID

5707

Gene nameproteasome 26S subunit, non-ATPase 1
Gene AliasP112
Cytomap2q37.1
Gene Typeprotein-coding
GO ID

GO:0006508

UniProtAcc

Q99460


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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
5707PSMD1HTA11_1938_2000001011HumanColorectumAD5.08e-065.73e-01-0.0811
5707PSMD1HTA11_347_2000001011HumanColorectumAD1.31e-033.50e-01-0.1954
5707PSMD1A015-C-203HumanColorectumFAP3.78e-21-3.55e-01-0.1294
5707PSMD1A015-C-204HumanColorectumFAP4.17e-05-3.00e-01-0.0228
5707PSMD1A002-C-201HumanColorectumFAP6.29e-05-2.41e-010.0324
5707PSMD1A002-C-203HumanColorectumFAP1.42e-03-1.29e-010.2786
5707PSMD1A001-C-119HumanColorectumFAP2.73e-05-3.95e-01-0.1557
5707PSMD1A001-C-108HumanColorectumFAP2.34e-15-2.87e-01-0.0272
5707PSMD1A002-C-205HumanColorectumFAP7.58e-12-3.77e-01-0.1236
5707PSMD1A001-C-104HumanColorectumFAP3.97e-03-2.33e-010.0184
5707PSMD1A015-C-006HumanColorectumFAP1.43e-06-2.85e-01-0.0994
5707PSMD1A015-C-106HumanColorectumFAP6.35e-07-2.46e-01-0.0511
5707PSMD1A002-C-114HumanColorectumFAP1.20e-10-4.16e-01-0.1561
5707PSMD1A015-C-104HumanColorectumFAP7.00e-24-4.08e-01-0.1899
5707PSMD1A001-C-014HumanColorectumFAP1.34e-07-2.98e-010.0135
5707PSMD1A002-C-016HumanColorectumFAP2.07e-13-2.93e-010.0521
5707PSMD1A015-C-002HumanColorectumFAP1.82e-05-3.29e-01-0.0763
5707PSMD1A001-C-203HumanColorectumFAP9.21e-09-2.73e-01-0.0481
5707PSMD1A002-C-116HumanColorectumFAP3.27e-22-4.00e-01-0.0452
5707PSMD1A014-C-008HumanColorectumFAP8.57e-10-5.06e-01-0.191
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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
Oral cavityOSCCGO 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).
Oral cavityLPGO 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).
Oral cavityEOLPGO 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).
Oral cavityNEOLPGO 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).
EsophagusHGINGO 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:0042176ColorectumADregulation of protein catabolic process160/3918391/187231.06e-197.34e-17160
GO:0010498ColorectumADproteasomal protein catabolic process174/3918490/187233.18e-147.66e-12174
GO:0043161ColorectumADproteasome-mediated ubiquitin-dependent protein catabolic process141/3918412/187231.77e-101.68e-08141
GO:00421764ColorectumFAPregulation of protein catabolic process106/2622391/187235.00e-123.06e-09106
GO:00431614ColorectumFAPproteasome-mediated ubiquitin-dependent protein catabolic process98/2622412/187235.41e-084.20e-0698
GO:00104984ColorectumFAPproteasomal protein catabolic process110/2622490/187232.12e-071.26e-05110
GO:0048863ColorectumFAPstem cell differentiation44/2622206/187232.48e-031.96e-0244
GO:00421765ColorectumCRCregulation of protein catabolic process87/2078391/187231.30e-106.49e-0887
GO:00431615ColorectumCRCproteasome-mediated ubiquitin-dependent protein catabolic process69/2078412/187233.16e-044.90e-0369
GO:00104985ColorectumCRCproteasomal protein catabolic process77/2078490/187231.03e-031.21e-0277
GO:00488635EndometriumAEHstem cell differentiation40/2100206/187233.67e-043.99e-0340
GO:001049817EndometriumEECproteasomal protein catabolic process112/2168490/187236.99e-131.40e-10112
GO:004316117EndometriumEECproteasome-mediated ubiquitin-dependent protein catabolic process92/2168412/187233.01e-103.23e-0892
GO:004886314EndometriumEECstem cell differentiation43/2168206/187238.48e-051.21e-0343
GO:004217627EsophagusHGINregulation of protein catabolic process119/2587391/187238.09e-182.43e-15119
GO:001049826EsophagusHGINproteasomal protein catabolic process139/2587490/187231.20e-173.41e-15139
GO:004586227EsophagusHGINpositive regulation of proteolysis107/2587372/187232.61e-144.60e-12107
GO:004316126EsophagusHGINproteasome-mediated ubiquitin-dependent protein catabolic process114/2587412/187237.00e-141.20e-11114
GO:190336227EsophagusHGINregulation of cellular protein catabolic process81/2587255/187231.16e-131.93e-1181
GO:190332027EsophagusHGINregulation of protein modification by small protein conjugation or removal78/2587242/187231.40e-132.26e-1178
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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
hsa050128ColorectumFAPParkinson disease80/1404266/84652.04e-086.20e-073.77e-0780
hsa050108ColorectumFAPAlzheimer disease105/1404384/84653.74e-081.04e-066.33e-07105
hsa050228ColorectumFAPPathways of neurodegeneration - multiple diseases117/1404476/84652.81e-064.47e-052.72e-05117
hsa050148ColorectumFAPAmyotrophic lateral sclerosis91/1404364/84651.84e-052.36e-041.44e-0491
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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
PSMD1SNVMissense_Mutationrs745401053c.164N>Ap.Arg55Glnp.R55QQ99460protein_codingtolerated(0.19)benign(0)TCGA-A2-A04P-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapytaxolPD
PSMD1SNVMissense_Mutationc.2809N>Ap.Glu937Lysp.E937KQ99460protein_codingtolerated(0.74)possibly_damaging(0.899)TCGA-AC-A23H-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownPD
PSMD1SNVMissense_Mutationc.2812N>Ap.Glu938Lysp.E938KQ99460protein_codingtolerated(0.7)possibly_damaging(0.899)TCGA-BH-A0B5-01Breastbreast invasive carcinomaFemale<65III/IVChemotherapyadriamycinCR
PSMD1SNVMissense_Mutationc.2755N>Cp.Glu919Glnp.E919QQ99460protein_codingtolerated(0.14)possibly_damaging(0.543)TCGA-D8-A1J8-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapynolvadexSD
PSMD1SNVMissense_Mutationc.2098G>Ap.Glu700Lysp.E700KQ99460protein_codingdeleterious(0.02)benign(0.141)TCGA-D8-A27G-01Breastbreast invasive carcinomaFemale>=65I/IIUnknownUnknownSD
PSMD1SNVMissense_Mutationc.898N>Cp.Glu300Glnp.E300QQ99460protein_codingtolerated(0.24)benign(0.001)TCGA-E2-A10C-01Breastbreast invasive carcinomaFemale<65I/IIChemotherapycytoxanSD
PSMD1SNVMissense_Mutationc.2177C>Ap.Ala726Aspp.A726DQ99460protein_codingdeleterious(0)probably_damaging(0.923)TCGA-E9-A295-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
PSMD1insertionFrame_Shift_Insnovelc.850dupAp.Thr284AsnfsTer12p.T284Nfs*12Q99460protein_codingTCGA-A2-A0EN-01Breastbreast invasive carcinomaFemale>=65I/IIHormone TherapytamoxiphenSD
PSMD1insertionFrame_Shift_Insnovelc.2407_2408insCTTTTCTTp.Lys803ThrfsTer36p.K803Tfs*36Q99460protein_codingTCGA-AC-A3QQ-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownSD
PSMD1insertionFrame_Shift_Insnovelc.268_269insCp.Val90AlafsTer3p.V90Afs*3Q99460protein_codingTCGA-B6-A0I8-01Breastbreast invasive carcinomaFemale<65I/IIUnknownUnknownPD
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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
5707PSMD1NAOPROZOMIBOPROZOMIB
5707PSMD1NAinhibitorCHEMBL325041BORTEZOMIB
5707PSMD1NAinhibitorCARFILZOMIBCARFILZOMIB
5707PSMD1NABORTEZOMIBBORTEZOMIB24524217
5707PSMD1NAinhibitorCHEMBL2103884OPROZOMIB
5707PSMD1NABORTEZOMIBBORTEZOMIB
5707PSMD1NABORTEZOMIBBORTEZOMIB
5707PSMD1NACARFILZOMIBCARFILZOMIB24524217
5707PSMD1NAMLN-9708IXAZOMIB CITRATE
5707PSMD1NAinhibitorCHEMBL451887CARFILZOMIB
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