|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: SKIV2L |
Gene summary for SKIV2L |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SKIV2L | Gene ID | 6499 |
| Gene name | Ski2 like RNA helicase | |
| Gene Alias | 170A | |
| Cytomap | 6p21.33 | |
| Gene Type | protein-coding | GO ID | GO:0000184 | UniProtAcc | A0A1U9X8J1 |
Top |
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 |
| 6499 | SKIV2L | LZE4T | Human | Esophagus | ESCC | 2.02e-03 | 1.26e-01 | 0.0811 |
| 6499 | SKIV2L | LZE7T | Human | Esophagus | ESCC | 1.78e-10 | 3.79e-01 | 0.0667 |
| 6499 | SKIV2L | LZE8T | Human | Esophagus | ESCC | 3.68e-07 | 1.43e-01 | 0.067 |
| 6499 | SKIV2L | LZE20T | Human | Esophagus | ESCC | 3.70e-08 | 1.51e-01 | 0.0662 |
| 6499 | SKIV2L | LZE24T | Human | Esophagus | ESCC | 2.64e-15 | 3.13e-01 | 0.0596 |
| 6499 | SKIV2L | LZE6T | Human | Esophagus | ESCC | 2.39e-02 | 1.36e-01 | 0.0845 |
| 6499 | SKIV2L | P1T-E | Human | Esophagus | ESCC | 2.78e-12 | 3.63e-01 | 0.0875 |
| 6499 | SKIV2L | P2T-E | Human | Esophagus | ESCC | 1.14e-13 | 2.52e-01 | 0.1177 |
| 6499 | SKIV2L | P4T-E | Human | Esophagus | ESCC | 3.01e-08 | 1.67e-01 | 0.1323 |
| 6499 | SKIV2L | P5T-E | Human | Esophagus | ESCC | 3.61e-07 | 9.10e-02 | 0.1327 |
| 6499 | SKIV2L | P8T-E | Human | Esophagus | ESCC | 2.70e-08 | 1.86e-01 | 0.0889 |
| 6499 | SKIV2L | P9T-E | Human | Esophagus | ESCC | 7.61e-11 | 1.79e-01 | 0.1131 |
| 6499 | SKIV2L | P10T-E | Human | Esophagus | ESCC | 1.80e-16 | 2.44e-01 | 0.116 |
| 6499 | SKIV2L | P11T-E | Human | Esophagus | ESCC | 2.08e-16 | 3.66e-01 | 0.1426 |
| 6499 | SKIV2L | P12T-E | Human | Esophagus | ESCC | 1.80e-12 | 2.42e-01 | 0.1122 |
| 6499 | SKIV2L | P15T-E | Human | Esophagus | ESCC | 1.74e-12 | 1.33e-01 | 0.1149 |
| 6499 | SKIV2L | P16T-E | Human | Esophagus | ESCC | 1.66e-10 | 1.97e-01 | 0.1153 |
| 6499 | SKIV2L | P17T-E | Human | Esophagus | ESCC | 4.26e-10 | 3.65e-01 | 0.1278 |
| 6499 | SKIV2L | P19T-E | Human | Esophagus | ESCC | 6.27e-07 | 3.99e-01 | 0.1662 |
| 6499 | SKIV2L | P20T-E | Human | Esophagus | ESCC | 2.70e-20 | 1.73e-01 | 0.1124 |
| Page: 1 2 3 4 5 |
| 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. |
Top |
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:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:0006402110 | Esophagus | ESCC | mRNA catabolic process | 170/8552 | 232/18723 | 8.70e-18 | 8.00e-16 | 170 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:000095618 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process | 88/8552 | 112/18723 | 9.41e-13 | 4.14e-11 | 88 |
| GO:000018414 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 32/8552 | 37/18723 | 2.96e-07 | 4.23e-06 | 32 |
| GO:00002913 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process, exonucleolytic | 18/8552 | 19/18723 | 8.00e-06 | 7.78e-05 | 18 |
| GO:00344271 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' | 10/8552 | 11/18723 | 2.54e-03 | 1.08e-02 | 10 |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
| GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
| GO:000640121 | Liver | HCC | RNA catabolic process | 201/7958 | 278/18723 | 3.88e-24 | 1.02e-21 | 201 |
| GO:003465521 | Liver | HCC | nucleobase-containing compound catabolic process | 273/7958 | 407/18723 | 4.84e-24 | 1.23e-21 | 273 |
| GO:000640221 | Liver | HCC | mRNA catabolic process | 169/7958 | 232/18723 | 4.50e-21 | 6.96e-19 | 169 |
| GO:000095621 | Liver | HCC | nuclear-transcribed mRNA catabolic process | 84/7958 | 112/18723 | 2.54e-12 | 1.18e-10 | 84 |
| GO:000018411 | Liver | HCC | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 29/7958 | 37/18723 | 9.37e-06 | 1.09e-04 | 29 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa030182 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
| hsa030183 | Liver | HCC | RNA degradation | 58/4020 | 79/8465 | 2.29e-06 | 2.19e-05 | 1.22e-05 | 58 |
| hsa030189 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| hsa0301814 | Oral cavity | OSCC | RNA degradation | 59/3704 | 79/8465 | 2.05e-08 | 1.91e-07 | 9.70e-08 | 59 |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| SKIV2L | SNV | Missense_Mutation | c.1364N>T | p.Ala455Val | p.A455V | Q15477 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SKIV2L | SNV | Missense_Mutation | rs746481824 | c.58N>T | p.Arg20Trp | p.R20W | Q15477 | protein_coding | deleterious(0.01) | benign(0.18) | TCGA-AO-A0JC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD |
| SKIV2L | SNV | Missense_Mutation | novel | c.2267N>C | p.Arg756Pro | p.R756P | Q15477 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD |
| SKIV2L | SNV | Missense_Mutation | rs746481824 | c.58C>T | p.Arg20Trp | p.R20W | Q15477 | protein_coding | deleterious(0.01) | benign(0.18) | TCGA-B6-A3ZX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| SKIV2L | SNV | Missense_Mutation | c.197N>T | p.Pro66Leu | p.P66L | Q15477 | protein_coding | tolerated(0.07) | benign(0.17) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| SKIV2L | SNV | Missense_Mutation | c.2332N>C | p.Asp778His | p.D778H | Q15477 | protein_coding | tolerated(0.17) | benign(0.157) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SKIV2L | SNV | Missense_Mutation | rs375183559 | c.3623N>A | p.Arg1208His | p.R1208H | Q15477 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SKIV2L | insertion | In_Frame_Ins | novel | c.2269_2270insGCACATGCCACACAGGCCTGGCTAATTTTTTTTTTTTTT | p.Val757delinsGlyThrCysHisThrGlyLeuAlaAsnPhePhePhePheLeu | p.V757delinsGTCHTGLANFFFFL | Q15477 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| SKIV2L | deletion | Frame_Shift_Del | novel | c.709delN | p.Arg238GlufsTer23 | p.R238Efs*23 | Q15477 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| SKIV2L | deletion | Frame_Shift_Del | novel | c.2311delN | p.Ser771LeufsTer19 | p.S771Lfs*19 | Q15477 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |