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Gene: SKP2 |
Gene summary for SKP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SKP2 | Gene ID | 6502 |
| Gene name | S-phase kinase associated protein 2 | |
| Gene Alias | FBL1 | |
| Cytomap | 5p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000082 | UniProtAcc | Q13309 |
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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 |
| 6502 | SKP2 | LZE4T | Human | Esophagus | ESCC | 1.83e-06 | 2.31e-01 | 0.0811 |
| 6502 | SKP2 | LZE7T | Human | Esophagus | ESCC | 2.12e-05 | 4.71e-01 | 0.0667 |
| 6502 | SKP2 | LZE8T | Human | Esophagus | ESCC | 7.53e-04 | 2.65e-01 | 0.067 |
| 6502 | SKP2 | LZE20T | Human | Esophagus | ESCC | 6.33e-03 | 1.66e-01 | 0.0662 |
| 6502 | SKP2 | LZE24T | Human | Esophagus | ESCC | 5.92e-04 | 1.91e-01 | 0.0596 |
| 6502 | SKP2 | LZE6T | Human | Esophagus | ESCC | 1.80e-10 | 6.53e-01 | 0.0845 |
| 6502 | SKP2 | P1T-E | Human | Esophagus | ESCC | 1.70e-04 | 2.39e-01 | 0.0875 |
| 6502 | SKP2 | P2T-E | Human | Esophagus | ESCC | 5.35e-23 | 4.53e-01 | 0.1177 |
| 6502 | SKP2 | P4T-E | Human | Esophagus | ESCC | 4.41e-15 | 4.39e-01 | 0.1323 |
| 6502 | SKP2 | P5T-E | Human | Esophagus | ESCC | 5.11e-05 | 1.79e-01 | 0.1327 |
| 6502 | SKP2 | P8T-E | Human | Esophagus | ESCC | 7.99e-12 | 2.68e-01 | 0.0889 |
| 6502 | SKP2 | P9T-E | Human | Esophagus | ESCC | 3.15e-03 | 1.08e-01 | 0.1131 |
| 6502 | SKP2 | P10T-E | Human | Esophagus | ESCC | 8.08e-38 | 7.52e-01 | 0.116 |
| 6502 | SKP2 | P11T-E | Human | Esophagus | ESCC | 8.61e-08 | 4.45e-01 | 0.1426 |
| 6502 | SKP2 | P12T-E | Human | Esophagus | ESCC | 9.23e-11 | 2.45e-01 | 0.1122 |
| 6502 | SKP2 | P15T-E | Human | Esophagus | ESCC | 3.60e-04 | 1.54e-01 | 0.1149 |
| 6502 | SKP2 | P16T-E | Human | Esophagus | ESCC | 2.84e-18 | 3.30e-01 | 0.1153 |
| 6502 | SKP2 | P17T-E | Human | Esophagus | ESCC | 4.81e-07 | 3.66e-01 | 0.1278 |
| 6502 | SKP2 | P20T-E | Human | Esophagus | ESCC | 2.43e-11 | 3.70e-01 | 0.1124 |
| 6502 | SKP2 | P21T-E | Human | Esophagus | ESCC | 1.50e-25 | 6.24e-01 | 0.1617 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | 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 |
| 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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:0043161111 | Esophagus | ESCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 312/8552 | 412/18723 | 3.53e-36 | 4.48e-33 | 312 |
| GO:1903320111 | Esophagus | ESCC | regulation of protein modification by small protein conjugation or removal | 181/8552 | 242/18723 | 1.80e-20 | 2.60e-18 | 181 |
| GO:004477216 | Esophagus | ESCC | mitotic cell cycle phase transition | 281/8552 | 424/18723 | 4.63e-18 | 4.45e-16 | 281 |
| GO:000020917 | Esophagus | ESCC | protein polyubiquitination | 170/8552 | 236/18723 | 1.40e-16 | 1.09e-14 | 170 |
| GO:0031396111 | Esophagus | ESCC | regulation of protein ubiquitination | 154/8552 | 210/18723 | 2.70e-16 | 2.04e-14 | 154 |
| GO:0071496111 | Esophagus | ESCC | cellular response to external stimulus | 215/8552 | 320/18723 | 4.29e-15 | 2.43e-13 | 215 |
| GO:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
| GO:0031668111 | Esophagus | ESCC | cellular response to extracellular stimulus | 168/8552 | 246/18723 | 4.93e-13 | 2.23e-11 | 168 |
| GO:007093617 | Esophagus | ESCC | protein K48-linked ubiquitination | 55/8552 | 65/18723 | 8.42e-11 | 2.58e-09 | 55 |
| GO:00516075 | Esophagus | ESCC | defense response to virus | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| GO:01405465 | Esophagus | ESCC | defense response to symbiont | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| GO:190332216 | Esophagus | ESCC | positive regulation of protein modification by small protein conjugation or removal | 99/8552 | 138/18723 | 4.39e-10 | 1.16e-08 | 99 |
| GO:0030522110 | Esophagus | ESCC | intracellular receptor signaling pathway | 170/8552 | 265/18723 | 8.58e-10 | 2.09e-08 | 170 |
| GO:00448394 | Esophagus | ESCC | cell cycle G2/M phase transition | 103/8552 | 148/18723 | 3.09e-09 | 6.67e-08 | 103 |
| GO:00000864 | Esophagus | ESCC | G2/M transition of mitotic cell cycle | 96/8552 | 137/18723 | 6.00e-09 | 1.23e-07 | 96 |
| GO:0048545111 | Esophagus | ESCC | response to steroid hormone | 204/8552 | 339/18723 | 4.47e-08 | 8.11e-07 | 204 |
| GO:003139816 | Esophagus | ESCC | positive regulation of protein ubiquitination | 82/8552 | 119/18723 | 2.41e-07 | 3.64e-06 | 82 |
| GO:000008214 | Esophagus | ESCC | G1/S transition of mitotic cell cycle | 134/8552 | 214/18723 | 4.04e-07 | 5.55e-06 | 134 |
| GO:004484314 | Esophagus | ESCC | cell cycle G1/S phase transition | 148/8552 | 241/18723 | 5.68e-07 | 7.48e-06 | 148 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0412027 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa0411023 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa05169210 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
| hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa052229 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
| hsa040689 | Esophagus | ESCC | FoxO signaling pathway | 89/4205 | 131/8465 | 1.56e-05 | 7.98e-05 | 4.09e-05 | 89 |
| hsa041505 | Esophagus | ESCC | mTOR signaling pathway | 98/4205 | 156/8465 | 5.81e-04 | 1.95e-03 | 9.97e-04 | 98 |
| hsa0412036 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa0411033 | Esophagus | ESCC | Cell cycle | 126/4205 | 157/8465 | 1.34e-15 | 5.60e-14 | 2.87e-14 | 126 |
| hsa0516937 | Esophagus | ESCC | Epstein-Barr virus infection | 151/4205 | 202/8465 | 1.55e-13 | 3.45e-12 | 1.77e-12 | 151 |
| hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
| hsa0522216 | Esophagus | ESCC | Small cell lung cancer | 69/4205 | 92/8465 | 5.40e-07 | 3.85e-06 | 1.97e-06 | 69 |
| hsa0406814 | Esophagus | ESCC | FoxO signaling pathway | 89/4205 | 131/8465 | 1.56e-05 | 7.98e-05 | 4.09e-05 | 89 |
| hsa0415013 | Esophagus | ESCC | mTOR signaling pathway | 98/4205 | 156/8465 | 5.81e-04 | 1.95e-03 | 9.97e-04 | 98 |
| hsa0412041 | Liver | HCC | Ubiquitin mediated proteolysis | 110/4020 | 142/8465 | 1.67e-13 | 3.74e-12 | 2.08e-12 | 110 |
| hsa041102 | Liver | HCC | Cell cycle | 106/4020 | 157/8465 | 2.54e-07 | 3.04e-06 | 1.69e-06 | 106 |
| hsa0516921 | Liver | HCC | Epstein-Barr virus infection | 128/4020 | 202/8465 | 3.17e-06 | 2.79e-05 | 1.55e-05 | 128 |
| hsa040684 | Liver | HCC | FoxO signaling pathway | 85/4020 | 131/8465 | 3.99e-05 | 2.16e-04 | 1.20e-04 | 85 |
| hsa041502 | Liver | HCC | mTOR signaling pathway | 95/4020 | 156/8465 | 4.70e-04 | 1.99e-03 | 1.11e-03 | 95 |
| hsa052032 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
| Page: 1 2 3 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| SKP2 | SNV | Missense_Mutation | novel | c.28N>A | p.Pro10Thr | p.P10T | Q13309 | protein_coding | deleterious(0.01) | benign(0.232) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SKP2 | insertion | Frame_Shift_Ins | novel | c.665_666insTTTAAAGCCTATGGTAGGTTATCTGTGCAGTGTGGGA | p.Val223LeufsTer26 | p.V223Lfs*26 | Q13309 | protein_coding | TCGA-AO-A0J2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||
| SKP2 | SNV | Missense_Mutation | c.484N>T | p.Ala162Ser | p.A162S | Q13309 | protein_coding | tolerated(0.34) | benign(0.034) | TCGA-AA-3855-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| SKP2 | SNV | Missense_Mutation | rs752559772 | c.535N>G | p.Ser179Gly | p.S179G | Q13309 | protein_coding | tolerated(0.39) | benign(0.001) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD |
| SKP2 | SNV | Missense_Mutation | novel | c.313N>T | p.Leu105Phe | p.L105F | Q13309 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SKP2 | SNV | Missense_Mutation | rs759798637 | c.674N>T | p.Thr225Ile | p.T225I | Q13309 | protein_coding | deleterious(0.01) | benign(0.03) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SKP2 | SNV | Missense_Mutation | novel | c.66N>T | p.Trp22Cys | p.W22C | Q13309 | protein_coding | deleterious(0.05) | probably_damaging(0.956) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SKP2 | SNV | Missense_Mutation | novel | c.987N>T | p.Gln329His | p.Q329H | Q13309 | protein_coding | tolerated(0.18) | benign(0.143) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| SKP2 | SNV | Missense_Mutation | novel | c.234N>A | p.Asp78Glu | p.D78E | Q13309 | protein_coding | tolerated(0.23) | benign(0.007) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SKP2 | SNV | Missense_Mutation | novel | c.247N>T | p.Arg83Cys | p.R83C | Q13309 | protein_coding | tolerated(0.06) | benign(0.045) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| Page: 1 2 3 4 |
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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 |
| Page: 1 |
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