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Gene: USP39 |
Gene summary for USP39 |
Gene summary. |
Gene information | Species | Human | Gene symbol | USP39 | Gene ID | 10713 |
Gene name | ubiquitin specific peptidase 39 | |
Gene Alias | 65K | |
Cytomap | 2p11.2 | |
Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | Q53GS9 |
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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 |
10713 | USP39 | P47T-E | Human | Esophagus | ESCC | 1.21e-17 | 3.45e-01 | 0.1067 |
10713 | USP39 | P48T-E | Human | Esophagus | ESCC | 7.52e-23 | 3.91e-01 | 0.0959 |
10713 | USP39 | P49T-E | Human | Esophagus | ESCC | 1.97e-18 | 1.30e+00 | 0.1768 |
10713 | USP39 | P52T-E | Human | Esophagus | ESCC | 2.12e-29 | 8.50e-01 | 0.1555 |
10713 | USP39 | P54T-E | Human | Esophagus | ESCC | 1.16e-20 | 4.73e-01 | 0.0975 |
10713 | USP39 | P56T-E | Human | Esophagus | ESCC | 1.03e-10 | 1.16e+00 | 0.1613 |
10713 | USP39 | P57T-E | Human | Esophagus | ESCC | 3.53e-16 | 3.53e-01 | 0.0926 |
10713 | USP39 | P61T-E | Human | Esophagus | ESCC | 2.71e-17 | 4.92e-01 | 0.099 |
10713 | USP39 | P62T-E | Human | Esophagus | ESCC | 1.08e-47 | 7.37e-01 | 0.1302 |
10713 | USP39 | P65T-E | Human | Esophagus | ESCC | 6.08e-26 | 4.74e-01 | 0.0978 |
10713 | USP39 | P74T-E | Human | Esophagus | ESCC | 1.22e-50 | 1.49e+00 | 0.1479 |
10713 | USP39 | P75T-E | Human | Esophagus | ESCC | 1.81e-42 | 8.39e-01 | 0.1125 |
10713 | USP39 | P76T-E | Human | Esophagus | ESCC | 5.65e-30 | 6.67e-01 | 0.1207 |
10713 | USP39 | P79T-E | Human | Esophagus | ESCC | 5.90e-37 | 7.30e-01 | 0.1154 |
10713 | USP39 | P80T-E | Human | Esophagus | ESCC | 2.71e-50 | 1.34e+00 | 0.155 |
10713 | USP39 | P82T-E | Human | Esophagus | ESCC | 1.55e-15 | 7.71e-01 | 0.1072 |
10713 | USP39 | P83T-E | Human | Esophagus | ESCC | 6.27e-59 | 1.38e+00 | 0.1738 |
10713 | USP39 | P84T-E | Human | Esophagus | ESCC | 1.81e-12 | 7.71e-01 | 0.0933 |
10713 | USP39 | P89T-E | Human | Esophagus | ESCC | 1.18e-15 | 1.08e+00 | 0.1752 |
10713 | USP39 | P91T-E | Human | Esophagus | ESCC | 1.78e-20 | 1.63e+00 | 0.1828 |
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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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
GO:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
GO:007064612 | Esophagus | ESCC | protein modification by small protein removal | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
GO:000024514 | Esophagus | ESCC | spliceosomal complex assembly | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
GO:00165793 | Esophagus | ESCC | protein deubiquitination | 79/8552 | 139/18723 | 5.23e-03 | 1.97e-02 | 79 |
GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
GO:000838022 | Liver | HCC | RNA splicing | 313/7958 | 434/18723 | 1.36e-36 | 1.73e-33 | 313 |
GO:000037522 | Liver | HCC | RNA splicing, via transesterification reactions | 228/7958 | 324/18723 | 1.47e-24 | 4.06e-22 | 228 |
GO:000037722 | Liver | HCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 224/7958 | 320/18723 | 1.16e-23 | 2.62e-21 | 224 |
GO:000039822 | Liver | HCC | mRNA splicing, via spliceosome | 224/7958 | 320/18723 | 1.16e-23 | 2.62e-21 | 224 |
GO:007182622 | Liver | HCC | ribonucleoprotein complex subunit organization | 159/7958 | 227/18723 | 3.14e-17 | 3.06e-15 | 159 |
GO:002261822 | Liver | HCC | ribonucleoprotein complex assembly | 153/7958 | 220/18723 | 3.44e-16 | 2.91e-14 | 153 |
GO:00706461 | Liver | HCC | protein modification by small protein removal | 91/7958 | 157/18723 | 6.50e-05 | 5.92e-04 | 91 |
GO:00165791 | Liver | HCC | protein deubiquitination | 78/7958 | 139/18723 | 8.13e-04 | 4.87e-03 | 78 |
GO:000024511 | Liver | HCC | spliceosomal complex assembly | 46/7958 | 79/18723 | 3.45e-03 | 1.56e-02 | 46 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
hsa0304022 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
hsa0304032 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
hsa0304016 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
hsa0304017 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
hsa0304026 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
hsa0304036 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
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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 |
USP39 | SNV | Missense_Mutation | c.786N>G | p.Ile262Met | p.I262M | Q53GS9 | protein_coding | tolerated(0.11) | possibly_damaging(0.544) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
USP39 | SNV | Missense_Mutation | novel | c.863N>A | p.Arg288Gln | p.R288Q | Q53GS9 | protein_coding | deleterious(0.03) | possibly_damaging(0.701) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
USP39 | SNV | Missense_Mutation | c.344N>C | p.Val115Ala | p.V115A | Q53GS9 | protein_coding | tolerated(0.07) | benign(0.038) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
USP39 | SNV | Missense_Mutation | c.1235N>G | p.Gln412Arg | p.Q412R | Q53GS9 | protein_coding | deleterious(0) | probably_damaging(0.955) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
USP39 | SNV | Missense_Mutation | rs769633859 | c.569C>T | p.Thr190Met | p.T190M | Q53GS9 | protein_coding | tolerated(0.07) | benign(0.134) | TCGA-EW-A3U0-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
USP39 | SNV | Missense_Mutation | c.469G>A | p.Val157Ile | p.V157I | Q53GS9 | protein_coding | deleterious(0.04) | possibly_damaging(0.531) | TCGA-GI-A2C8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Adriamycin | SD | |
USP39 | insertion | Nonsense_Mutation | novel | c.429_430insGGCTAGGAATACCTAACTTCCTGGGAATGCAGCCTGTCAAGGCC | p.Gln144GlyfsTer2 | p.Q144Gfs*2 | Q53GS9 | protein_coding | TCGA-A8-A0A4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR | ||
USP39 | deletion | Frame_Shift_Del | novel | c.722delN | p.Gln241ArgfsTer40 | p.Q241Rfs*40 | Q53GS9 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
USP39 | SNV | Missense_Mutation | rs749981625 | c.1544G>A | p.Arg515Gln | p.R515Q | Q53GS9 | protein_coding | deleterious(0) | possibly_damaging(0.731) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
USP39 | SNV | Missense_Mutation | novel | c.121G>A | p.Ala41Thr | p.A41T | Q53GS9 | protein_coding | tolerated_low_confidence(0.62) | benign(0) | TCGA-IR-A3LL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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 |
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