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Gene: PSMD1 |
Gene summary for PSMD1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PSMD1 | Gene ID | 5707 |
Gene name | proteasome 26S subunit, non-ATPase 1 | |
Gene Alias | P112 | |
Cytomap | 2q37.1 | |
Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q99460 |
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Malignant transformation analysis |
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 |
Malignant transformation involving gene list. |
Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
5707 | PSMD1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.08e-06 | 5.73e-01 | -0.0811 |
5707 | PSMD1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.31e-03 | 3.50e-01 | -0.1954 |
5707 | PSMD1 | A015-C-203 | Human | Colorectum | FAP | 3.78e-21 | -3.55e-01 | -0.1294 |
5707 | PSMD1 | A015-C-204 | Human | Colorectum | FAP | 4.17e-05 | -3.00e-01 | -0.0228 |
5707 | PSMD1 | A002-C-201 | Human | Colorectum | FAP | 6.29e-05 | -2.41e-01 | 0.0324 |
5707 | PSMD1 | A002-C-203 | Human | Colorectum | FAP | 1.42e-03 | -1.29e-01 | 0.2786 |
5707 | PSMD1 | A001-C-119 | Human | Colorectum | FAP | 2.73e-05 | -3.95e-01 | -0.1557 |
5707 | PSMD1 | A001-C-108 | Human | Colorectum | FAP | 2.34e-15 | -2.87e-01 | -0.0272 |
5707 | PSMD1 | A002-C-205 | Human | Colorectum | FAP | 7.58e-12 | -3.77e-01 | -0.1236 |
5707 | PSMD1 | A001-C-104 | Human | Colorectum | FAP | 3.97e-03 | -2.33e-01 | 0.0184 |
5707 | PSMD1 | A015-C-006 | Human | Colorectum | FAP | 1.43e-06 | -2.85e-01 | -0.0994 |
5707 | PSMD1 | A015-C-106 | Human | Colorectum | FAP | 6.35e-07 | -2.46e-01 | -0.0511 |
5707 | PSMD1 | A002-C-114 | Human | Colorectum | FAP | 1.20e-10 | -4.16e-01 | -0.1561 |
5707 | PSMD1 | A015-C-104 | Human | Colorectum | FAP | 7.00e-24 | -4.08e-01 | -0.1899 |
5707 | PSMD1 | A001-C-014 | Human | Colorectum | FAP | 1.34e-07 | -2.98e-01 | 0.0135 |
5707 | PSMD1 | A002-C-016 | Human | Colorectum | FAP | 2.07e-13 | -2.93e-01 | 0.0521 |
5707 | PSMD1 | A015-C-002 | Human | Colorectum | FAP | 1.82e-05 | -3.29e-01 | -0.0763 |
5707 | PSMD1 | A001-C-203 | Human | Colorectum | FAP | 9.21e-09 | -2.73e-01 | -0.0481 |
5707 | PSMD1 | A002-C-116 | Human | Colorectum | FAP | 3.27e-22 | -4.00e-01 | -0.0452 |
5707 | PSMD1 | A014-C-008 | Human | Colorectum | FAP | 8.57e-10 | -5.06e-01 | -0.191 |
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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. |
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Malignant transformation related pathway analysis |
Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
Figure of enriched GO biological processes. |
Tissue | Disease Stage | Enriched GO biological Processes |
Colorectum | AD | |
Colorectum | SER | |
Colorectum | MSS | |
Colorectum | MSI-H | |
Colorectum | FAP |
∗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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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0042176 | Colorectum | AD | regulation of protein catabolic process | 160/3918 | 391/18723 | 1.06e-19 | 7.34e-17 | 160 |
GO:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
GO:0043161 | Colorectum | AD | proteasome-mediated ubiquitin-dependent protein catabolic process | 141/3918 | 412/18723 | 1.77e-10 | 1.68e-08 | 141 |
GO:00421764 | Colorectum | FAP | regulation of protein catabolic process | 106/2622 | 391/18723 | 5.00e-12 | 3.06e-09 | 106 |
GO:00431614 | Colorectum | FAP | proteasome-mediated ubiquitin-dependent protein catabolic process | 98/2622 | 412/18723 | 5.41e-08 | 4.20e-06 | 98 |
GO:00104984 | Colorectum | FAP | proteasomal protein catabolic process | 110/2622 | 490/18723 | 2.12e-07 | 1.26e-05 | 110 |
GO:0048863 | Colorectum | FAP | stem cell differentiation | 44/2622 | 206/18723 | 2.48e-03 | 1.96e-02 | 44 |
GO:00421765 | Colorectum | CRC | regulation of protein catabolic process | 87/2078 | 391/18723 | 1.30e-10 | 6.49e-08 | 87 |
GO:00431615 | Colorectum | CRC | proteasome-mediated ubiquitin-dependent protein catabolic process | 69/2078 | 412/18723 | 3.16e-04 | 4.90e-03 | 69 |
GO:00104985 | Colorectum | CRC | proteasomal protein catabolic process | 77/2078 | 490/18723 | 1.03e-03 | 1.21e-02 | 77 |
GO:00488635 | Endometrium | AEH | stem cell differentiation | 40/2100 | 206/18723 | 3.67e-04 | 3.99e-03 | 40 |
GO:001049817 | Endometrium | EEC | proteasomal protein catabolic process | 112/2168 | 490/18723 | 6.99e-13 | 1.40e-10 | 112 |
GO:004316117 | Endometrium | EEC | proteasome-mediated ubiquitin-dependent protein catabolic process | 92/2168 | 412/18723 | 3.01e-10 | 3.23e-08 | 92 |
GO:004886314 | Endometrium | EEC | stem cell differentiation | 43/2168 | 206/18723 | 8.48e-05 | 1.21e-03 | 43 |
GO:004217627 | Esophagus | HGIN | regulation of protein catabolic process | 119/2587 | 391/18723 | 8.09e-18 | 2.43e-15 | 119 |
GO:001049826 | Esophagus | HGIN | proteasomal protein catabolic process | 139/2587 | 490/18723 | 1.20e-17 | 3.41e-15 | 139 |
GO:004586227 | Esophagus | HGIN | positive regulation of proteolysis | 107/2587 | 372/18723 | 2.61e-14 | 4.60e-12 | 107 |
GO:004316126 | Esophagus | HGIN | proteasome-mediated ubiquitin-dependent protein catabolic process | 114/2587 | 412/18723 | 7.00e-14 | 1.20e-11 | 114 |
GO:190336227 | Esophagus | HGIN | regulation of cellular protein catabolic process | 81/2587 | 255/18723 | 1.16e-13 | 1.93e-11 | 81 |
GO:190332027 | Esophagus | HGIN | regulation of protein modification by small protein conjugation or removal | 78/2587 | 242/18723 | 1.40e-13 | 2.26e-11 | 78 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0516943 | Oral cavity | EOLP | Epstein-Barr virus infection | 66/1218 | 202/8465 | 2.23e-11 | 1.20e-09 | 7.08e-10 | 66 |
hsa0501245 | Oral cavity | EOLP | Parkinson disease | 75/1218 | 266/8465 | 2.26e-09 | 5.62e-08 | 3.32e-08 | 75 |
hsa0501445 | Oral cavity | EOLP | Amyotrophic lateral sclerosis | 93/1218 | 364/8465 | 7.07e-09 | 1.14e-07 | 6.74e-08 | 93 |
hsa0502245 | Oral cavity | EOLP | Pathways of neurodegeneration - multiple diseases | 110/1218 | 476/8465 | 1.09e-07 | 1.26e-06 | 7.40e-07 | 110 |
hsa0502045 | Oral cavity | EOLP | Prion disease | 70/1218 | 273/8465 | 4.73e-07 | 4.78e-06 | 2.82e-06 | 70 |
hsa0501045 | Oral cavity | EOLP | Alzheimer disease | 87/1218 | 384/8465 | 5.79e-06 | 3.67e-05 | 2.16e-05 | 87 |
hsa0501645 | Oral cavity | EOLP | Huntington disease | 69/1218 | 306/8465 | 6.32e-05 | 2.96e-04 | 1.75e-04 | 69 |
hsa0501742 | Oral cavity | EOLP | Spinocerebellar ataxia | 30/1218 | 143/8465 | 1.96e-02 | 4.94e-02 | 2.91e-02 | 30 |
hsa0516953 | Oral cavity | EOLP | Epstein-Barr virus infection | 66/1218 | 202/8465 | 2.23e-11 | 1.20e-09 | 7.08e-10 | 66 |
hsa0501255 | Oral cavity | EOLP | Parkinson disease | 75/1218 | 266/8465 | 2.26e-09 | 5.62e-08 | 3.32e-08 | 75 |
hsa0501455 | Oral cavity | EOLP | Amyotrophic lateral sclerosis | 93/1218 | 364/8465 | 7.07e-09 | 1.14e-07 | 6.74e-08 | 93 |
hsa0502255 | Oral cavity | EOLP | Pathways of neurodegeneration - multiple diseases | 110/1218 | 476/8465 | 1.09e-07 | 1.26e-06 | 7.40e-07 | 110 |
hsa0502055 | Oral cavity | EOLP | Prion disease | 70/1218 | 273/8465 | 4.73e-07 | 4.78e-06 | 2.82e-06 | 70 |
hsa0501055 | Oral cavity | EOLP | Alzheimer disease | 87/1218 | 384/8465 | 5.79e-06 | 3.67e-05 | 2.16e-05 | 87 |
hsa0501655 | Oral cavity | EOLP | Huntington disease | 69/1218 | 306/8465 | 6.32e-05 | 2.96e-04 | 1.75e-04 | 69 |
hsa0501752 | Oral cavity | EOLP | Spinocerebellar ataxia | 30/1218 | 143/8465 | 1.96e-02 | 4.94e-02 | 2.91e-02 | 30 |
hsa0501262 | Oral cavity | NEOLP | Parkinson disease | 78/1112 | 266/8465 | 1.34e-12 | 1.06e-10 | 6.68e-11 | 78 |
hsa0501462 | Oral cavity | NEOLP | Amyotrophic lateral sclerosis | 95/1112 | 364/8465 | 8.76e-12 | 3.98e-10 | 2.50e-10 | 95 |
hsa0501062 | Oral cavity | NEOLP | Alzheimer disease | 97/1112 | 384/8465 | 3.97e-11 | 1.57e-09 | 9.89e-10 | 97 |
hsa0502262 | Oral cavity | NEOLP | Pathways of neurodegeneration - multiple diseases | 112/1112 | 476/8465 | 1.33e-10 | 3.84e-09 | 2.41e-09 | 112 |
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Cell-cell communication analysis |
Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon 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 |
Annotation of somatic variants for genes involved in malignant transformation |
Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
PSMD1 | SNV | Missense_Mutation | rs745401053 | c.164N>A | p.Arg55Gln | p.R55Q | Q99460 | protein_coding | tolerated(0.19) | benign(0) | TCGA-A2-A04P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | PD |
PSMD1 | SNV | Missense_Mutation | c.2809N>A | p.Glu937Lys | p.E937K | Q99460 | protein_coding | tolerated(0.74) | possibly_damaging(0.899) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
PSMD1 | SNV | Missense_Mutation | c.2812N>A | p.Glu938Lys | p.E938K | Q99460 | protein_coding | tolerated(0.7) | possibly_damaging(0.899) | TCGA-BH-A0B5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR | |
PSMD1 | SNV | Missense_Mutation | c.2755N>C | p.Glu919Gln | p.E919Q | Q99460 | protein_coding | tolerated(0.14) | possibly_damaging(0.543) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
PSMD1 | SNV | Missense_Mutation | c.2098G>A | p.Glu700Lys | p.E700K | Q99460 | protein_coding | deleterious(0.02) | benign(0.141) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PSMD1 | SNV | Missense_Mutation | c.898N>C | p.Glu300Gln | p.E300Q | Q99460 | protein_coding | tolerated(0.24) | benign(0.001) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
PSMD1 | SNV | Missense_Mutation | c.2177C>A | p.Ala726Asp | p.A726D | Q99460 | protein_coding | deleterious(0) | probably_damaging(0.923) | TCGA-E9-A295-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
PSMD1 | insertion | Frame_Shift_Ins | novel | c.850dupA | p.Thr284AsnfsTer12 | p.T284Nfs*12 | Q99460 | protein_coding | TCGA-A2-A0EN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
PSMD1 | insertion | Frame_Shift_Ins | novel | c.2407_2408insCTTTTCTT | p.Lys803ThrfsTer36 | p.K803Tfs*36 | Q99460 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
PSMD1 | insertion | Frame_Shift_Ins | novel | c.268_269insC | p.Val90AlafsTer3 | p.V90Afs*3 | Q99460 | protein_coding | TCGA-B6-A0I8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
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Related drugs of malignant transformation related genes |
Identification of chemicals and drugs interact with genes involved in malignant transfromation |
(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
5707 | PSMD1 | NA | OPROZOMIB | OPROZOMIB | ||
5707 | PSMD1 | NA | inhibitor | CHEMBL325041 | BORTEZOMIB | |
5707 | PSMD1 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB | |
5707 | PSMD1 | NA | BORTEZOMIB | BORTEZOMIB | 24524217 | |
5707 | PSMD1 | NA | inhibitor | CHEMBL2103884 | OPROZOMIB | |
5707 | PSMD1 | NA | BORTEZOMIB | BORTEZOMIB | ||
5707 | PSMD1 | NA | BORTEZOMIB | BORTEZOMIB | ||
5707 | PSMD1 | NA | CARFILZOMIB | CARFILZOMIB | 24524217 | |
5707 | PSMD1 | NA | MLN-9708 | IXAZOMIB CITRATE | ||
5707 | PSMD1 | NA | inhibitor | CHEMBL451887 | CARFILZOMIB |
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