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Gene: SKAP2 |
Gene summary for SKAP2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SKAP2 | Gene ID | 8935 |
Gene name | src kinase associated phosphoprotein 2 | |
Gene Alias | PRAP | |
Cytomap | 7p15.2 | |
Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | B7Z5R3 |
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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 |
8935 | SKAP2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.63e-06 | -3.81e-01 | 0.0155 |
8935 | SKAP2 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.29e-04 | 4.01e-01 | -0.1954 |
8935 | SKAP2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.48e-02 | -2.65e-01 | -0.1207 |
8935 | SKAP2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.34e-05 | -3.72e-01 | 0.294 |
8935 | SKAP2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.23e-09 | -4.26e-01 | 0.3005 |
8935 | SKAP2 | A001-C-207 | Human | Colorectum | FAP | 1.52e-04 | -4.06e-01 | 0.1278 |
8935 | SKAP2 | A015-C-203 | Human | Colorectum | FAP | 3.43e-20 | -4.12e-01 | -0.1294 |
8935 | SKAP2 | A002-C-201 | Human | Colorectum | FAP | 1.75e-09 | -4.27e-01 | 0.0324 |
8935 | SKAP2 | A001-C-119 | Human | Colorectum | FAP | 3.27e-07 | -5.17e-01 | -0.1557 |
8935 | SKAP2 | A001-C-108 | Human | Colorectum | FAP | 3.59e-13 | -3.47e-01 | -0.0272 |
8935 | SKAP2 | A002-C-205 | Human | Colorectum | FAP | 3.54e-15 | -4.70e-01 | -0.1236 |
8935 | SKAP2 | A001-C-104 | Human | Colorectum | FAP | 1.17e-03 | -3.17e-01 | 0.0184 |
8935 | SKAP2 | A015-C-005 | Human | Colorectum | FAP | 1.08e-06 | -4.00e-01 | -0.0336 |
8935 | SKAP2 | A015-C-006 | Human | Colorectum | FAP | 7.03e-13 | -5.20e-01 | -0.0994 |
8935 | SKAP2 | A015-C-106 | Human | Colorectum | FAP | 6.51e-11 | -3.53e-01 | -0.0511 |
8935 | SKAP2 | A002-C-114 | Human | Colorectum | FAP | 1.71e-12 | -4.89e-01 | -0.1561 |
8935 | SKAP2 | A015-C-104 | Human | Colorectum | FAP | 1.38e-23 | -4.89e-01 | -0.1899 |
8935 | SKAP2 | A001-C-014 | Human | Colorectum | FAP | 3.76e-12 | -3.88e-01 | 0.0135 |
8935 | SKAP2 | A002-C-016 | Human | Colorectum | FAP | 7.29e-17 | -3.00e-01 | 0.0521 |
8935 | SKAP2 | A015-C-002 | Human | Colorectum | FAP | 7.92e-08 | -4.28e-01 | -0.0763 |
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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:00421132 | Oral cavity | EOLP | B cell activation | 61/2218 | 334/18723 | 3.68e-04 | 3.35e-03 | 61 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05135 | Colorectum | AD | Yersinia infection | 58/2092 | 137/8465 | 3.90e-06 | 4.35e-05 | 2.78e-05 | 58 |
hsa051351 | Colorectum | AD | Yersinia infection | 58/2092 | 137/8465 | 3.90e-06 | 4.35e-05 | 2.78e-05 | 58 |
hsa051354 | Colorectum | MSS | Yersinia infection | 53/1875 | 137/8465 | 7.73e-06 | 8.93e-05 | 5.47e-05 | 53 |
hsa051355 | Colorectum | MSS | Yersinia infection | 53/1875 | 137/8465 | 7.73e-06 | 8.93e-05 | 5.47e-05 | 53 |
hsa051356 | Colorectum | FAP | Yersinia infection | 43/1404 | 137/8465 | 1.21e-05 | 1.62e-04 | 9.86e-05 | 43 |
hsa051357 | Colorectum | FAP | Yersinia infection | 43/1404 | 137/8465 | 1.21e-05 | 1.62e-04 | 9.86e-05 | 43 |
hsa0513526 | Esophagus | ESCC | Yersinia infection | 100/4205 | 137/8465 | 1.80e-08 | 1.59e-07 | 8.12e-08 | 100 |
hsa05135111 | Esophagus | ESCC | Yersinia infection | 100/4205 | 137/8465 | 1.80e-08 | 1.59e-07 | 8.12e-08 | 100 |
hsa0513542 | Liver | HCC | Yersinia infection | 92/4020 | 137/8465 | 2.25e-06 | 2.19e-05 | 1.22e-05 | 92 |
hsa0513552 | Liver | HCC | Yersinia infection | 92/4020 | 137/8465 | 2.25e-06 | 2.19e-05 | 1.22e-05 | 92 |
hsa0513520 | Oral cavity | OSCC | Yersinia infection | 94/3704 | 137/8465 | 2.85e-09 | 3.08e-08 | 1.57e-08 | 94 |
hsa05135110 | Oral cavity | OSCC | Yersinia infection | 94/3704 | 137/8465 | 2.85e-09 | 3.08e-08 | 1.57e-08 | 94 |
hsa0513544 | Oral cavity | EOLP | Yersinia infection | 44/1218 | 137/8465 | 8.88e-08 | 1.06e-06 | 6.27e-07 | 44 |
hsa0513554 | Oral cavity | EOLP | Yersinia infection | 44/1218 | 137/8465 | 8.88e-08 | 1.06e-06 | 6.27e-07 | 44 |
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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 |
SKAP2 | SNV | Missense_Mutation | c.689N>G | p.Tyr230Cys | p.Y230C | O75563 | protein_coding | deleterious(0.01) | benign(0.213) | TCGA-BC-A5W4-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD | |
SKAP2 | SNV | Missense_Mutation | c.725N>T | p.His242Leu | p.H242L | O75563 | protein_coding | tolerated(0.38) | benign(0.05) | TCGA-44-7670-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
SKAP2 | SNV | Missense_Mutation | novel | c.202G>T | p.Asp68Tyr | p.D68Y | O75563 | protein_coding | tolerated(0.09) | possibly_damaging(0.786) | TCGA-49-AAR2-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | taxol | CR |
SKAP2 | SNV | Missense_Mutation | rs371274766 | c.1062N>A | p.Met354Ile | p.M354I | O75563 | protein_coding | tolerated(0.23) | benign(0.017) | TCGA-55-8301-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | PR |
SKAP2 | SNV | Missense_Mutation | c.1003N>T | p.Gly335Cys | p.G335C | O75563 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-97-A4M7-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SKAP2 | SNV | Missense_Mutation | c.382A>G | p.Lys128Glu | p.K128E | O75563 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-21-1071-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
SKAP2 | SNV | Missense_Mutation | novel | c.469N>T | p.Asp157Tyr | p.D157Y | O75563 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-58-A46M-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SKAP2 | SNV | Missense_Mutation | c.808N>T | p.Asp270Tyr | p.D270Y | O75563 | protein_coding | deleterious(0) | benign(0.073) | TCGA-66-2770-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SKAP2 | SNV | Missense_Mutation | rs747450045 | c.959N>A | p.Arg320His | p.R320H | O75563 | protein_coding | deleterious(0.03) | benign(0.411) | TCGA-85-8355-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SKAP2 | SNV | Missense_Mutation | novel | c.25T>A | p.Ser9Thr | p.S9T | O75563 | protein_coding | tolerated_low_confidence(0.25) | benign(0) | TCGA-94-A5I4-01 | Lung | lung squamous cell carcinoma | Male | <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 |
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