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Gene: SS18L1 |
Gene summary for SS18L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SS18L1 | Gene ID | 26039 |
| Gene name | SS18L1 subunit of BAF chromatin remodeling complex | |
| Gene Alias | CREST | |
| Cytomap | 20q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O75177 |
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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 |
| 26039 | SS18L1 | LZE4T | Human | Esophagus | ESCC | 3.43e-02 | 1.22e-02 | 0.0811 |
| 26039 | SS18L1 | LZE20T | Human | Esophagus | ESCC | 2.13e-04 | 5.41e-02 | 0.0662 |
| 26039 | SS18L1 | LZE24T | Human | Esophagus | ESCC | 6.65e-07 | 5.87e-02 | 0.0596 |
| 26039 | SS18L1 | P1T-E | Human | Esophagus | ESCC | 2.69e-02 | 1.08e-01 | 0.0875 |
| 26039 | SS18L1 | P2T-E | Human | Esophagus | ESCC | 3.67e-04 | 5.12e-02 | 0.1177 |
| 26039 | SS18L1 | P4T-E | Human | Esophagus | ESCC | 3.30e-05 | 1.08e-02 | 0.1323 |
| 26039 | SS18L1 | P5T-E | Human | Esophagus | ESCC | 1.24e-07 | 3.69e-02 | 0.1327 |
| 26039 | SS18L1 | P8T-E | Human | Esophagus | ESCC | 2.05e-05 | 1.11e-02 | 0.0889 |
| 26039 | SS18L1 | P9T-E | Human | Esophagus | ESCC | 8.58e-08 | 3.83e-02 | 0.1131 |
| 26039 | SS18L1 | P10T-E | Human | Esophagus | ESCC | 6.55e-19 | 2.61e-01 | 0.116 |
| 26039 | SS18L1 | P12T-E | Human | Esophagus | ESCC | 2.15e-12 | 1.73e-01 | 0.1122 |
| 26039 | SS18L1 | P15T-E | Human | Esophagus | ESCC | 7.70e-12 | 8.11e-02 | 0.1149 |
| 26039 | SS18L1 | P16T-E | Human | Esophagus | ESCC | 1.29e-16 | 1.80e-01 | 0.1153 |
| 26039 | SS18L1 | P17T-E | Human | Esophagus | ESCC | 1.18e-03 | 1.14e-01 | 0.1278 |
| 26039 | SS18L1 | P20T-E | Human | Esophagus | ESCC | 4.19e-17 | 2.26e-01 | 0.1124 |
| 26039 | SS18L1 | P21T-E | Human | Esophagus | ESCC | 9.97e-11 | 4.20e-02 | 0.1617 |
| 26039 | SS18L1 | P22T-E | Human | Esophagus | ESCC | 4.30e-08 | 5.12e-02 | 0.1236 |
| 26039 | SS18L1 | P23T-E | Human | Esophagus | ESCC | 4.32e-08 | 1.30e-01 | 0.108 |
| 26039 | SS18L1 | P26T-E | Human | Esophagus | ESCC | 3.24e-06 | 4.85e-02 | 0.1276 |
| 26039 | SS18L1 | P27T-E | Human | Esophagus | ESCC | 2.77e-07 | 5.12e-02 | 0.1055 |
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| 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 |
| ∗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). |
| 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:000632517 | Esophagus | ESCC | chromatin organization | 240/8552 | 409/18723 | 6.52e-08 | 1.14e-06 | 240 |
| GO:002260420 | Esophagus | ESCC | regulation of cell morphogenesis | 180/8552 | 309/18723 | 5.19e-06 | 5.45e-05 | 180 |
| GO:003134616 | Esophagus | ESCC | positive regulation of cell projection organization | 201/8552 | 353/18723 | 1.19e-05 | 1.11e-04 | 201 |
| GO:001072010 | Esophagus | ESCC | positive regulation of cell development | 172/8552 | 298/18723 | 1.74e-05 | 1.55e-04 | 172 |
| GO:005076710 | Esophagus | ESCC | regulation of neurogenesis | 203/8552 | 364/18723 | 6.10e-05 | 4.68e-04 | 203 |
| GO:00507697 | Esophagus | ESCC | positive regulation of neurogenesis | 131/8552 | 225/18723 | 9.71e-05 | 6.90e-04 | 131 |
| GO:001097516 | Esophagus | ESCC | regulation of neuron projection development | 240/8552 | 445/18723 | 2.48e-04 | 1.53e-03 | 240 |
| GO:001076920 | Esophagus | ESCC | regulation of cell morphogenesis involved in differentiation | 61/8552 | 96/18723 | 3.12e-04 | 1.85e-03 | 61 |
| GO:00519606 | Esophagus | ESCC | regulation of nervous system development | 237/8552 | 443/18723 | 5.02e-04 | 2.78e-03 | 237 |
| GO:001077018 | Esophagus | ESCC | positive regulation of cell morphogenesis involved in differentiation | 51/8552 | 79/18723 | 5.48e-04 | 3.00e-03 | 51 |
| GO:00519625 | Esophagus | ESCC | positive regulation of nervous system development | 149/8552 | 272/18723 | 1.50e-03 | 7.06e-03 | 149 |
| GO:001635816 | Esophagus | ESCC | dendrite development | 130/8552 | 243/18723 | 8.33e-03 | 2.95e-02 | 130 |
| GO:00226047 | Liver | NAFLD | regulation of cell morphogenesis | 62/1882 | 309/18723 | 8.35e-08 | 7.09e-06 | 62 |
| GO:00107697 | Liver | NAFLD | regulation of cell morphogenesis involved in differentiation | 24/1882 | 96/18723 | 1.98e-05 | 5.62e-04 | 24 |
| GO:00163585 | Liver | NAFLD | dendrite development | 43/1882 | 243/18723 | 1.70e-04 | 3.07e-03 | 43 |
| GO:00313465 | Liver | NAFLD | positive regulation of cell projection organization | 57/1882 | 353/18723 | 2.19e-04 | 3.73e-03 | 57 |
| GO:00063255 | Liver | NAFLD | chromatin organization | 64/1882 | 409/18723 | 2.31e-04 | 3.89e-03 | 64 |
| GO:00107707 | Liver | NAFLD | positive regulation of cell morphogenesis involved in differentiation | 19/1882 | 79/18723 | 2.42e-04 | 4.06e-03 | 19 |
| GO:00488133 | Liver | NAFLD | dendrite morphogenesis | 29/1882 | 146/18723 | 2.63e-04 | 4.26e-03 | 29 |
| GO:00109755 | Liver | NAFLD | regulation of neuron projection development | 64/1882 | 445/18723 | 2.12e-03 | 2.08e-02 | 64 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052028 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0520213 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| SS18L1 | SNV | Missense_Mutation | rs140015301 | c.464N>T | p.Ala155Val | p.A155V | O75177 | protein_coding | tolerated_low_confidence(0.05) | benign(0.06) | TCGA-A2-A0CO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR |
| SS18L1 | SNV | Missense_Mutation | novel | c.298N>T | p.His100Tyr | p.H100Y | O75177 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SS18L1 | SNV | Missense_Mutation | novel | c.1064A>G | p.Tyr355Cys | p.Y355C | O75177 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.996) | TCGA-HM-A6W2-06 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| SS18L1 | SNV | Missense_Mutation | novel | c.758N>G | p.Tyr253Cys | p.Y253C | O75177 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.997) | TCGA-VS-A9V4-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| SS18L1 | SNV | Missense_Mutation | c.791C>T | p.Ala264Val | p.A264V | O75177 | protein_coding | deleterious_low_confidence(0.02) | benign(0.06) | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | |
| SS18L1 | SNV | Missense_Mutation | novel | c.1142N>G | p.Gln381Arg | p.Q381R | O75177 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.953) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SS18L1 | SNV | Missense_Mutation | c.1088N>A | p.Gly363Asp | p.G363D | O75177 | protein_coding | deleterious_low_confidence(0) | benign(0.43) | TCGA-CM-5860-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | SD | |
| SS18L1 | SNV | Missense_Mutation | rs746253864 | c.143C>T | p.Thr48Met | p.T48M | O75177 | protein_coding | deleterious(0.04) | benign(0.369) | TCGA-F4-6463-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| SS18L1 | SNV | Missense_Mutation | novel | c.875N>G | p.Asp292Gly | p.D292G | O75177 | protein_coding | deleterious_low_confidence(0.04) | possibly_damaging(0.629) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SS18L1 | SNV | Missense_Mutation | rs753325512 | c.610G>A | p.Gly204Ser | p.G204S | O75177 | protein_coding | tolerated_low_confidence(0.06) | possibly_damaging(0.747) | TCGA-EI-6882-01 | Colorectum | rectum 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 |
| Page: 1 |
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