|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: SFSWAP |
Gene summary for SFSWAP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SFSWAP | Gene ID | 6433 |
| Gene name | splicing factor SWAP | |
| Gene Alias | SFRS8 | |
| Cytomap | 12q24.33 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | Q12872 |
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 |
| 6433 | SFSWAP | LZE4T | Human | Esophagus | ESCC | 2.05e-09 | 1.41e-01 | 0.0811 |
| 6433 | SFSWAP | LZE5T | Human | Esophagus | ESCC | 2.69e-03 | 3.01e-01 | 0.0514 |
| 6433 | SFSWAP | LZE7T | Human | Esophagus | ESCC | 3.48e-09 | 4.94e-01 | 0.0667 |
| 6433 | SFSWAP | LZE20T | Human | Esophagus | ESCC | 5.22e-04 | 1.53e-01 | 0.0662 |
| 6433 | SFSWAP | LZE22T | Human | Esophagus | ESCC | 9.56e-06 | 4.69e-01 | 0.068 |
| 6433 | SFSWAP | LZE24T | Human | Esophagus | ESCC | 4.70e-18 | 3.40e-01 | 0.0596 |
| 6433 | SFSWAP | LZE6T | Human | Esophagus | ESCC | 4.69e-05 | 1.57e-01 | 0.0845 |
| 6433 | SFSWAP | P1T-E | Human | Esophagus | ESCC | 1.31e-15 | 7.71e-01 | 0.0875 |
| 6433 | SFSWAP | P2T-E | Human | Esophagus | ESCC | 7.82e-52 | 1.02e+00 | 0.1177 |
| 6433 | SFSWAP | P4T-E | Human | Esophagus | ESCC | 1.01e-24 | 5.05e-01 | 0.1323 |
| 6433 | SFSWAP | P5T-E | Human | Esophagus | ESCC | 3.13e-23 | 4.85e-01 | 0.1327 |
| 6433 | SFSWAP | P8T-E | Human | Esophagus | ESCC | 4.11e-33 | 5.31e-01 | 0.0889 |
| 6433 | SFSWAP | P9T-E | Human | Esophagus | ESCC | 9.91e-14 | 2.28e-01 | 0.1131 |
| 6433 | SFSWAP | P10T-E | Human | Esophagus | ESCC | 8.10e-26 | 4.53e-01 | 0.116 |
| 6433 | SFSWAP | P11T-E | Human | Esophagus | ESCC | 6.75e-20 | 7.45e-01 | 0.1426 |
| 6433 | SFSWAP | P12T-E | Human | Esophagus | ESCC | 4.21e-18 | 4.74e-01 | 0.1122 |
| 6433 | SFSWAP | P15T-E | Human | Esophagus | ESCC | 3.55e-30 | 5.59e-01 | 0.1149 |
| 6433 | SFSWAP | P16T-E | Human | Esophagus | ESCC | 4.68e-30 | 5.47e-01 | 0.1153 |
| 6433 | SFSWAP | P17T-E | Human | Esophagus | ESCC | 4.33e-09 | 3.57e-01 | 0.1278 |
| 6433 | SFSWAP | P19T-E | Human | Esophagus | ESCC | 1.69e-07 | 6.06e-01 | 0.1662 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:190331233 | Oral cavity | NEOLP | negative regulation of mRNA metabolic process | 28/2005 | 92/18723 | 1.92e-07 | 6.49e-06 | 28 |
| GO:003311934 | Oral cavity | NEOLP | negative regulation of RNA splicing | 12/2005 | 25/18723 | 3.01e-06 | 6.82e-05 | 12 |
| GO:004802531 | Oral cavity | NEOLP | negative regulation of mRNA splicing, via spliceosome | 9/2005 | 20/18723 | 1.02e-04 | 1.23e-03 | 9 |
| GO:005068631 | Oral cavity | NEOLP | negative regulation of mRNA processing | 10/2005 | 29/18723 | 5.71e-04 | 4.96e-03 | 10 |
| GO:00063763 | Oral cavity | NEOLP | mRNA splice site selection | 12/2005 | 49/18723 | 4.66e-03 | 2.56e-02 | 12 |
| GO:000024531 | Oral cavity | NEOLP | spliceosomal complex assembly | 16/2005 | 79/18723 | 8.78e-03 | 4.21e-02 | 16 |
| GO:000838027 | Skin | AK | RNA splicing | 111/1910 | 434/18723 | 1.85e-20 | 5.49e-17 | 111 |
| GO:190331125 | Skin | AK | regulation of mRNA metabolic process | 81/1910 | 288/18723 | 7.27e-18 | 8.61e-15 | 81 |
| GO:004348428 | Skin | AK | regulation of RNA splicing | 54/1910 | 148/18723 | 9.66e-18 | 9.53e-15 | 54 |
| GO:002261328 | Skin | AK | ribonucleoprotein complex biogenesis | 108/1910 | 463/18723 | 8.48e-17 | 6.27e-14 | 108 |
| GO:000037526 | Skin | AK | RNA splicing, via transesterification reactions | 85/1910 | 324/18723 | 1.16e-16 | 7.62e-14 | 85 |
| GO:000037726 | Skin | AK | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 84/1910 | 320/18723 | 1.69e-16 | 9.11e-14 | 84 |
| GO:000039826 | Skin | AK | mRNA splicing, via spliceosome | 84/1910 | 320/18723 | 1.69e-16 | 9.11e-14 | 84 |
| GO:005068420 | Skin | AK | regulation of mRNA processing | 47/1910 | 137/18723 | 1.92e-14 | 7.57e-12 | 47 |
| GO:004802427 | Skin | AK | regulation of mRNA splicing, via spliceosome | 39/1910 | 101/18723 | 3.87e-14 | 1.43e-11 | 39 |
| GO:007182628 | Skin | AK | ribonucleoprotein complex subunit organization | 61/1910 | 227/18723 | 7.85e-13 | 2.02e-10 | 61 |
| GO:002261828 | Skin | AK | ribonucleoprotein complex assembly | 58/1910 | 220/18723 | 6.75e-12 | 1.33e-09 | 58 |
| GO:000038020 | Skin | AK | alternative mRNA splicing, via spliceosome | 30/1910 | 77/18723 | 2.57e-11 | 4.90e-09 | 30 |
| GO:190331227 | Skin | AK | negative regulation of mRNA metabolic process | 25/1910 | 92/18723 | 3.50e-06 | 8.86e-05 | 25 |
| GO:003311927 | Skin | AK | negative regulation of RNA splicing | 11/1910 | 25/18723 | 1.39e-05 | 2.73e-04 | 11 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| SFSWAP | SNV | Missense_Mutation | novel | c.1058C>G | p.Ser353Cys | p.S353C | Q12872 | protein_coding | deleterious(0.01) | possibly_damaging(0.741) | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD |
| SFSWAP | SNV | Missense_Mutation | c.1903G>C | p.Glu635Gln | p.E635Q | Q12872 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| SFSWAP | SNV | Missense_Mutation | novel | c.1015A>T | p.Thr339Ser | p.T339S | Q12872 | protein_coding | tolerated(0.48) | benign(0.007) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| SFSWAP | SNV | Missense_Mutation | novel | c.1136G>T | p.Cys379Phe | p.C379F | Q12872 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-B6-A2IU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| SFSWAP | SNV | Missense_Mutation | novel | c.865N>A | p.Asp289Asn | p.D289N | Q12872 | protein_coding | deleterious(0.03) | probably_damaging(0.962) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD |
| SFSWAP | SNV | Missense_Mutation | c.1903N>A | p.Glu635Lys | p.E635K | Q12872 | protein_coding | deleterious(0.04) | probably_damaging(0.99) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| SFSWAP | SNV | Missense_Mutation | novel | c.204N>T | p.Lys68Asn | p.K68N | Q12872 | protein_coding | tolerated(0.33) | benign(0.054) | TCGA-E2-A1IK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| SFSWAP | SNV | Missense_Mutation | c.1157N>A | p.Gly386Glu | p.G386E | Q12872 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SFSWAP | insertion | Frame_Shift_Ins | novel | c.1704_1705insATATTTTTGCCATCTCCTAATAAAGA | p.Gly569IlefsTer13 | p.G569Ifs*13 | Q12872 | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SFSWAP | insertion | Nonsense_Mutation | novel | c.2939_2940insAGTATAA | p.Thr981ValfsTer2 | p.T981Vfs*2 | Q12872 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
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 |