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Gene: SKP1 |
Gene summary for SKP1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SKP1 | Gene ID | 6500 |
Gene name | S-phase kinase associated protein 1 | |
Gene Alias | EMC19 | |
Cytomap | 5q31.1 | |
Gene Type | protein-coding | GO ID | GO:0000209 | UniProtAcc | P63208 |
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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 |
6500 | SKP1 | GSM4909286 | Human | Breast | IDC | 2.73e-07 | -1.34e-01 | 0.1081 |
6500 | SKP1 | GSM4909288 | Human | Breast | IDC | 4.46e-02 | -2.51e-03 | 0.0988 |
6500 | SKP1 | GSM4909293 | Human | Breast | IDC | 5.41e-12 | 3.17e-01 | 0.1581 |
6500 | SKP1 | GSM4909294 | Human | Breast | IDC | 1.52e-36 | 3.43e-01 | 0.2022 |
6500 | SKP1 | GSM4909296 | Human | Breast | IDC | 2.02e-13 | -9.03e-02 | 0.1524 |
6500 | SKP1 | GSM4909297 | Human | Breast | IDC | 9.41e-37 | 5.68e-02 | 0.1517 |
6500 | SKP1 | GSM4909298 | Human | Breast | IDC | 4.21e-05 | 2.60e-01 | 0.1551 |
6500 | SKP1 | GSM4909299 | Human | Breast | IDC | 3.98e-05 | 2.14e-01 | 0.035 |
6500 | SKP1 | GSM4909300 | Human | Breast | IDC | 9.16e-03 | 2.58e-01 | 0.0334 |
6500 | SKP1 | GSM4909302 | Human | Breast | IDC | 2.07e-04 | -2.79e-01 | 0.1545 |
6500 | SKP1 | GSM4909305 | Human | Breast | IDC | 3.07e-07 | 3.01e-01 | 0.0436 |
6500 | SKP1 | GSM4909306 | Human | Breast | IDC | 6.40e-12 | 2.94e-01 | 0.1564 |
6500 | SKP1 | GSM4909307 | Human | Breast | IDC | 2.06e-15 | 2.92e-01 | 0.1569 |
6500 | SKP1 | GSM4909308 | Human | Breast | IDC | 1.01e-37 | 4.82e-01 | 0.158 |
6500 | SKP1 | GSM4909309 | Human | Breast | IDC | 1.64e-17 | 1.82e-01 | 0.0483 |
6500 | SKP1 | GSM4909311 | Human | Breast | IDC | 1.94e-65 | -5.43e-01 | 0.1534 |
6500 | SKP1 | GSM4909312 | Human | Breast | IDC | 2.97e-13 | -1.48e-01 | 0.1552 |
6500 | SKP1 | GSM4909313 | Human | Breast | IDC | 1.38e-06 | 9.38e-02 | 0.0391 |
6500 | SKP1 | GSM4909315 | Human | Breast | IDC | 2.12e-23 | 2.77e-01 | 0.21 |
6500 | SKP1 | GSM4909316 | Human | Breast | IDC | 1.29e-16 | 2.57e-01 | 0.21 |
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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:007093610 | Esophagus | HGIN | protein K48-linked ubiquitination | 24/2587 | 65/18723 | 2.69e-06 | 9.49e-05 | 24 |
GO:000020916 | Esophagus | HGIN | protein polyubiquitination | 58/2587 | 236/18723 | 6.29e-06 | 1.97e-04 | 58 |
GO:005165126 | Esophagus | HGIN | maintenance of location in cell | 53/2587 | 214/18723 | 1.22e-05 | 3.45e-04 | 53 |
GO:005123520 | Esophagus | HGIN | maintenance of location | 73/2587 | 327/18723 | 1.73e-05 | 4.71e-04 | 73 |
GO:004518523 | Esophagus | HGIN | maintenance of protein location | 28/2587 | 94/18723 | 4.52e-05 | 1.09e-03 | 28 |
GO:00165708 | Esophagus | HGIN | histone modification | 92/2587 | 463/18723 | 1.70e-04 | 3.30e-03 | 92 |
GO:19033228 | Esophagus | HGIN | positive regulation of protein modification by small protein conjugation or removal | 35/2587 | 138/18723 | 2.11e-04 | 3.88e-03 | 35 |
GO:003250719 | Esophagus | HGIN | maintenance of protein location in cell | 20/2587 | 65/18723 | 3.31e-04 | 5.48e-03 | 20 |
GO:00165747 | Esophagus | HGIN | histone ubiquitination | 16/2587 | 47/18723 | 3.61e-04 | 5.68e-03 | 16 |
GO:00514575 | Esophagus | HGIN | maintenance of protein location in nucleus | 10/2587 | 23/18723 | 5.09e-04 | 7.38e-03 | 10 |
GO:00725959 | Esophagus | HGIN | maintenance of protein localization in organelle | 14/2587 | 42/18723 | 1.05e-03 | 1.31e-02 | 14 |
GO:00335225 | Esophagus | HGIN | histone H2A ubiquitination | 10/2587 | 26/18723 | 1.60e-03 | 1.79e-02 | 10 |
GO:190466620 | Esophagus | HGIN | regulation of ubiquitin protein ligase activity | 9/2587 | 23/18723 | 2.37e-03 | 2.40e-02 | 9 |
GO:00313987 | Esophagus | HGIN | positive regulation of protein ubiquitination | 28/2587 | 119/18723 | 2.89e-03 | 2.81e-02 | 28 |
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:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
GO:003450418 | Esophagus | ESCC | protein localization to nucleus | 211/8552 | 290/18723 | 4.06e-21 | 6.60e-19 | 211 |
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:000020917 | Esophagus | ESCC | protein polyubiquitination | 170/8552 | 236/18723 | 1.40e-16 | 1.09e-14 | 170 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513218 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
hsa0513118 | Breast | Precancer | Shigellosis | 44/684 | 247/8465 | 3.91e-07 | 6.86e-06 | 5.26e-06 | 44 |
hsa0414118 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
hsa0513219 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
hsa0513119 | Breast | Precancer | Shigellosis | 44/684 | 247/8465 | 3.91e-07 | 6.86e-06 | 5.26e-06 | 44 |
hsa0414119 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
hsa0513224 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
hsa0513124 | Breast | IDC | Shigellosis | 47/867 | 247/8465 | 1.78e-05 | 2.00e-04 | 1.49e-04 | 47 |
hsa0414124 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa0517014 | Breast | IDC | Human immunodeficiency virus 1 infection | 33/867 | 212/8465 | 9.28e-03 | 4.37e-02 | 3.27e-02 | 33 |
hsa0513234 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
hsa0513134 | Breast | IDC | Shigellosis | 47/867 | 247/8465 | 1.78e-05 | 2.00e-04 | 1.49e-04 | 47 |
hsa0414134 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
hsa0517015 | Breast | IDC | Human immunodeficiency virus 1 infection | 33/867 | 212/8465 | 9.28e-03 | 4.37e-02 | 3.27e-02 | 33 |
hsa0513243 | Breast | DCIS | Salmonella infection | 55/846 | 249/8465 | 8.71e-09 | 1.87e-07 | 1.38e-07 | 55 |
hsa0414143 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
hsa0513144 | Breast | DCIS | Shigellosis | 46/846 | 247/8465 | 2.06e-05 | 2.38e-04 | 1.75e-04 | 46 |
hsa0517024 | Breast | DCIS | Human immunodeficiency virus 1 infection | 33/846 | 212/8465 | 6.49e-03 | 3.22e-02 | 2.37e-02 | 33 |
hsa0513253 | Breast | DCIS | Salmonella infection | 55/846 | 249/8465 | 8.71e-09 | 1.87e-07 | 1.38e-07 | 55 |
hsa0414153 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
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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 |
SKP1 | SNV | Missense_Mutation | novel | c.228G>C | p.Glu76Asp | p.E76D | P63208 | protein_coding | tolerated(0.54) | benign(0.005) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SKP1 | SNV | Missense_Mutation | novel | c.411N>T | p.Lys137Asn | p.K137N | P63208 | protein_coding | deleterious(0.04) | benign(0.158) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SKP1 | SNV | Missense_Mutation | novel | c.407G>C | p.Arg136Pro | p.R136P | P63208 | protein_coding | deleterious(0.01) | benign(0.012) | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SKP1 | SNV | Missense_Mutation | novel | c.406N>T | p.Arg136Cys | p.R136C | P63208 | protein_coding | deleterious(0.04) | benign(0.011) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
SKP1 | SNV | Missense_Mutation | novel | c.382N>C | p.Lys128Gln | p.K128Q | P63208 | protein_coding | deleterious(0) | possibly_damaging(0.656) | TCGA-D1-A1O8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
SKP1 | insertion | Frame_Shift_Ins | novel | c.226_227insCATCTTTATTATCTTTGCGTATAGCAATTCGTATTATTGGGCAAGAC | p.Glu76AlafsTer34 | p.E76Afs*34 | P63208 | protein_coding | TCGA-DD-A73E-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
SKP1 | SNV | Missense_Mutation | c.49N>T | p.Asp17Tyr | p.D17Y | P63208 | protein_coding | deleterious(0) | possibly_damaging(0.891) | TCGA-05-4382-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
SKP1 | SNV | Missense_Mutation | novel | c.239A>G | p.Lys80Arg | p.K80R | P63208 | protein_coding | tolerated(0.27) | possibly_damaging(0.899) | TCGA-05-4427-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | CR |
SKP1 | SNV | Missense_Mutation | novel | c.139N>G | p.Leu47Val | p.L47V | P63208 | protein_coding | tolerated(0.11) | probably_damaging(0.959) | TCGA-49-6742-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | alimta | PD |
SKP1 | SNV | Missense_Mutation | novel | c.317N>G | p.Ala106Gly | p.A106G | P63208 | protein_coding | deleterious(0) | possibly_damaging(0.698) | TCGA-55-8089-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
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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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