|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: SLF2 |
Gene summary for SLF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SLF2 | Gene ID | 55719 |
| Gene name | SMC5-SMC6 complex localization factor 2 | |
| Gene Alias | C10orf6 | |
| Cytomap | 10q24.31 | |
| Gene Type | protein-coding | GO ID | GO:0000070 | UniProtAcc | Q8IX21 |
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 |
| 55719 | SLF2 | LZE24T | Human | Esophagus | ESCC | 6.67e-15 | 2.50e-01 | 0.0596 |
| 55719 | SLF2 | P2T-E | Human | Esophagus | ESCC | 4.51e-08 | 1.90e-01 | 0.1177 |
| 55719 | SLF2 | P4T-E | Human | Esophagus | ESCC | 9.22e-08 | 1.81e-01 | 0.1323 |
| 55719 | SLF2 | P5T-E | Human | Esophagus | ESCC | 6.71e-11 | 2.30e-01 | 0.1327 |
| 55719 | SLF2 | P8T-E | Human | Esophagus | ESCC | 4.72e-12 | 2.31e-01 | 0.0889 |
| 55719 | SLF2 | P9T-E | Human | Esophagus | ESCC | 2.39e-03 | 1.27e-01 | 0.1131 |
| 55719 | SLF2 | P10T-E | Human | Esophagus | ESCC | 2.45e-08 | 1.10e-01 | 0.116 |
| 55719 | SLF2 | P11T-E | Human | Esophagus | ESCC | 1.49e-07 | 2.72e-01 | 0.1426 |
| 55719 | SLF2 | P12T-E | Human | Esophagus | ESCC | 2.41e-14 | 2.59e-01 | 0.1122 |
| 55719 | SLF2 | P15T-E | Human | Esophagus | ESCC | 9.78e-03 | 1.18e-01 | 0.1149 |
| 55719 | SLF2 | P16T-E | Human | Esophagus | ESCC | 6.66e-10 | 1.80e-01 | 0.1153 |
| 55719 | SLF2 | P20T-E | Human | Esophagus | ESCC | 3.11e-10 | 2.16e-01 | 0.1124 |
| 55719 | SLF2 | P21T-E | Human | Esophagus | ESCC | 3.85e-02 | 9.16e-02 | 0.1617 |
| 55719 | SLF2 | P22T-E | Human | Esophagus | ESCC | 1.23e-02 | 1.18e-01 | 0.1236 |
| 55719 | SLF2 | P23T-E | Human | Esophagus | ESCC | 3.15e-14 | 3.28e-01 | 0.108 |
| 55719 | SLF2 | P24T-E | Human | Esophagus | ESCC | 6.58e-04 | 1.04e-01 | 0.1287 |
| 55719 | SLF2 | P26T-E | Human | Esophagus | ESCC | 3.84e-11 | 1.44e-01 | 0.1276 |
| 55719 | SLF2 | P27T-E | Human | Esophagus | ESCC | 6.44e-10 | 2.38e-01 | 0.1055 |
| 55719 | SLF2 | P28T-E | Human | Esophagus | ESCC | 5.69e-09 | 1.91e-01 | 0.1149 |
| 55719 | SLF2 | P30T-E | Human | Esophagus | ESCC | 2.88e-06 | 2.07e-01 | 0.137 |
| 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 | ||
| 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:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:000007011 | Esophagus | ESCC | mitotic sister chromatid segregation | 138/8552 | 168/18723 | 1.37e-22 | 2.63e-20 | 138 |
| GO:00008194 | Esophagus | ESCC | sister chromatid segregation | 157/8552 | 202/18723 | 8.41e-21 | 1.33e-18 | 157 |
| GO:003304416 | Esophagus | ESCC | regulation of chromosome organization | 145/8552 | 187/18723 | 3.80e-19 | 4.31e-17 | 145 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:0043254111 | Esophagus | ESCC | regulation of protein-containing complex assembly | 278/8552 | 428/18723 | 3.81e-16 | 2.77e-14 | 278 |
| GO:0031334111 | Esophagus | ESCC | positive regulation of protein-containing complex assembly | 166/8552 | 237/18723 | 2.06e-14 | 1.07e-12 | 166 |
| GO:005105215 | Esophagus | ESCC | regulation of DNA metabolic process | 232/8552 | 359/18723 | 2.40e-13 | 1.13e-11 | 232 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| GO:00988133 | Esophagus | ESCC | nuclear chromosome segregation | 187/8552 | 281/18723 | 1.00e-12 | 4.36e-11 | 187 |
| GO:00002802 | Esophagus | ESCC | nuclear division | 270/8552 | 439/18723 | 1.17e-11 | 4.24e-10 | 270 |
| GO:005105417 | Esophagus | ESCC | positive regulation of DNA metabolic process | 139/8552 | 201/18723 | 1.20e-11 | 4.33e-10 | 139 |
| GO:2001020110 | Esophagus | ESCC | regulation of response to DNA damage stimulus | 145/8552 | 219/18723 | 5.97e-10 | 1.50e-08 | 145 |
| GO:004578710 | Esophagus | ESCC | positive regulation of cell cycle | 196/8552 | 313/18723 | 9.27e-10 | 2.24e-08 | 196 |
| GO:200125219 | Esophagus | ESCC | positive regulation of chromosome organization | 64/8552 | 82/18723 | 1.98e-09 | 4.52e-08 | 64 |
| GO:003450211 | Esophagus | ESCC | protein localization to chromosome | 70/8552 | 92/18723 | 2.54e-09 | 5.64e-08 | 70 |
| GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
| GO:00900689 | Esophagus | ESCC | positive regulation of cell cycle process | 142/8552 | 236/18723 | 4.79e-06 | 5.08e-05 | 142 |
| GO:20010228 | Esophagus | ESCC | positive regulation of response to DNA damage stimulus | 69/8552 | 105/18723 | 2.66e-05 | 2.22e-04 | 69 |
| GO:00062826 | Esophagus | ESCC | regulation of DNA repair | 82/8552 | 130/18723 | 4.65e-05 | 3.66e-04 | 82 |
| 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 |
| SLF2 | SNV | Missense_Mutation | novel | c.1189N>G | p.Ser397Gly | p.S397G | Q8IX21 | protein_coding | tolerated(0.45) | benign(0.006) | TCGA-A2-A1FZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Arimidex | SD |
| SLF2 | SNV | Missense_Mutation | novel | c.725C>T | p.Ser242Phe | p.S242F | Q8IX21 | protein_coding | deleterious(0) | benign(0.025) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| SLF2 | SNV | Missense_Mutation | novel | c.337N>A | p.Glu113Lys | p.E113K | Q8IX21 | protein_coding | tolerated(0.12) | benign(0.007) | TCGA-D8-A73U-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| SLF2 | SNV | Missense_Mutation | c.685N>C | p.Glu229Gln | p.E229Q | Q8IX21 | protein_coding | tolerated(0.11) | probably_damaging(0.947) | TCGA-E2-A1LG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| SLF2 | insertion | Nonsense_Mutation | novel | c.825_826insTACATGAGTCACGTCGGCCTTGTCTGTCACTAGCCTCC | p.Lys276TyrfsTer11 | p.K276Yfs*11 | Q8IX21 | protein_coding | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| SLF2 | SNV | Missense_Mutation | novel | c.577A>G | p.Thr193Ala | p.T193A | Q8IX21 | protein_coding | tolerated(0.48) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SLF2 | SNV | Missense_Mutation | novel | c.1412C>T | p.Thr471Ile | p.T471I | Q8IX21 | protein_coding | tolerated(0.51) | benign(0.084) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SLF2 | SNV | Missense_Mutation | rs747051897 | c.1636C>T | p.Arg546Cys | p.R546C | Q8IX21 | protein_coding | tolerated(0.2) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SLF2 | SNV | Missense_Mutation | c.1090N>A | p.Arg364Ser | p.R364S | Q8IX21 | protein_coding | tolerated(0.45) | benign(0.151) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD | |
| SLF2 | SNV | Missense_Mutation | novel | c.1708N>A | p.Ala570Thr | p.A570T | Q8IX21 | protein_coding | tolerated(0.88) | benign(0) | TCGA-C5-A7XC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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 |