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Gene: SRRT |
Gene summary for SRRT |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SRRT | Gene ID | 51593 |
| Gene name | serrate, RNA effector molecule | |
| Gene Alias | ARS2 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9BXP5 |
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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 |
| 51593 | SRRT | LZE4T | Human | Esophagus | ESCC | 1.17e-09 | 3.78e-01 | 0.0811 |
| 51593 | SRRT | LZE7T | Human | Esophagus | ESCC | 8.00e-14 | 7.79e-01 | 0.0667 |
| 51593 | SRRT | LZE8T | Human | Esophagus | ESCC | 9.28e-14 | 2.57e-01 | 0.067 |
| 51593 | SRRT | LZE20T | Human | Esophagus | ESCC | 3.37e-04 | 1.84e-01 | 0.0662 |
| 51593 | SRRT | LZE21D1 | Human | Esophagus | HGIN | 9.57e-03 | 2.26e-01 | 0.0632 |
| 51593 | SRRT | LZE22T | Human | Esophagus | ESCC | 1.27e-18 | 5.90e-01 | 0.068 |
| 51593 | SRRT | LZE24T | Human | Esophagus | ESCC | 4.12e-19 | 4.91e-01 | 0.0596 |
| 51593 | SRRT | LZE21T | Human | Esophagus | ESCC | 1.33e-03 | 5.75e-01 | 0.0655 |
| 51593 | SRRT | LZE6T | Human | Esophagus | ESCC | 1.63e-07 | 4.23e-01 | 0.0845 |
| 51593 | SRRT | P1T-E | Human | Esophagus | ESCC | 1.02e-14 | 7.65e-01 | 0.0875 |
| 51593 | SRRT | P2T-E | Human | Esophagus | ESCC | 2.48e-61 | 1.15e+00 | 0.1177 |
| 51593 | SRRT | P4T-E | Human | Esophagus | ESCC | 5.65e-23 | 6.35e-01 | 0.1323 |
| 51593 | SRRT | P5T-E | Human | Esophagus | ESCC | 6.72e-15 | 3.62e-01 | 0.1327 |
| 51593 | SRRT | P8T-E | Human | Esophagus | ESCC | 7.59e-29 | 6.05e-01 | 0.0889 |
| 51593 | SRRT | P9T-E | Human | Esophagus | ESCC | 1.55e-19 | 4.54e-01 | 0.1131 |
| 51593 | SRRT | P10T-E | Human | Esophagus | ESCC | 4.16e-30 | 6.51e-01 | 0.116 |
| 51593 | SRRT | P11T-E | Human | Esophagus | ESCC | 3.17e-16 | 6.20e-01 | 0.1426 |
| 51593 | SRRT | P12T-E | Human | Esophagus | ESCC | 1.13e-40 | 8.01e-01 | 0.1122 |
| 51593 | SRRT | P15T-E | Human | Esophagus | ESCC | 8.20e-33 | 8.48e-01 | 0.1149 |
| 51593 | SRRT | P16T-E | Human | Esophagus | ESCC | 3.37e-42 | 9.37e-01 | 0.1153 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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. |
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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:005076914 | Thyroid | PTC | positive regulation of neurogenesis | 105/5968 | 225/18723 | 2.28e-06 | 3.05e-05 | 105 |
| GO:005076716 | Thyroid | PTC | regulation of neurogenesis | 156/5968 | 364/18723 | 5.86e-06 | 7.05e-05 | 156 |
| GO:004668517 | Thyroid | PTC | response to arsenic-containing substance | 23/5968 | 33/18723 | 9.16e-06 | 1.04e-04 | 23 |
| GO:005196214 | Thyroid | PTC | positive regulation of nervous system development | 117/5968 | 272/18723 | 6.72e-05 | 5.89e-04 | 117 |
| GO:00519608 | Thyroid | PTC | regulation of nervous system development | 177/5968 | 443/18723 | 1.72e-04 | 1.32e-03 | 177 |
| GO:009872710 | Thyroid | PTC | maintenance of cell number | 63/5968 | 134/18723 | 1.73e-04 | 1.32e-03 | 63 |
| GO:00198279 | Thyroid | PTC | stem cell population maintenance | 61/5968 | 131/18723 | 3.01e-04 | 2.12e-03 | 61 |
| GO:003519616 | Thyroid | PTC | production of miRNAs involved in gene silencing by miRNA | 28/5968 | 52/18723 | 8.33e-04 | 5.13e-03 | 28 |
| GO:003105010 | Thyroid | PTC | dsRNA processing | 28/5968 | 54/18723 | 1.79e-03 | 9.68e-03 | 28 |
| GO:007091810 | Thyroid | PTC | production of small RNA involved in gene silencing by RNA | 28/5968 | 54/18723 | 1.79e-03 | 9.68e-03 | 28 |
| GO:003447021 | Thyroid | ATC | ncRNA processing | 216/6293 | 395/18723 | 3.14e-18 | 3.98e-16 | 216 |
| GO:003466021 | Thyroid | ATC | ncRNA metabolic process | 240/6293 | 485/18723 | 2.03e-13 | 9.91e-12 | 240 |
| GO:001072022 | Thyroid | ATC | positive regulation of cell development | 146/6293 | 298/18723 | 2.36e-08 | 4.56e-07 | 146 |
| GO:005076922 | Thyroid | ATC | positive regulation of neurogenesis | 112/6293 | 225/18723 | 3.53e-07 | 5.21e-06 | 112 |
| GO:005076723 | Thyroid | ATC | regulation of neurogenesis | 168/6293 | 364/18723 | 3.73e-07 | 5.48e-06 | 168 |
| GO:005196014 | Thyroid | ATC | regulation of nervous system development | 195/6293 | 443/18723 | 2.62e-06 | 3.06e-05 | 195 |
| GO:004668523 | Thyroid | ATC | response to arsenic-containing substance | 24/6293 | 33/18723 | 4.98e-06 | 5.40e-05 | 24 |
| GO:009872722 | Thyroid | ATC | maintenance of cell number | 70/6293 | 134/18723 | 6.45e-06 | 6.69e-05 | 70 |
| GO:005196221 | Thyroid | ATC | positive regulation of nervous system development | 126/6293 | 272/18723 | 8.17e-06 | 8.27e-05 | 126 |
| GO:001982722 | Thyroid | ATC | stem cell population maintenance | 67/6293 | 131/18723 | 2.48e-05 | 2.16e-04 | 67 |
| 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 |
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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 |
| SRRT | SNV | Missense_Mutation | c.367A>T | p.Met123Leu | p.M123L | Q9BXP5 | protein_coding | tolerated(0.73) | benign(0) | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SRRT | SNV | Missense_Mutation | c.2546N>G | p.Pro849Arg | p.P849R | Q9BXP5 | protein_coding | tolerated(0.15) | benign(0.151) | TCGA-A7-A0DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SRRT | SNV | Missense_Mutation | c.2467C>T | p.Pro823Ser | p.P823S | Q9BXP5 | protein_coding | tolerated(0.08) | benign(0.157) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| SRRT | SNV | Missense_Mutation | rs201528871 | c.1801N>T | p.Arg601Trp | p.R601W | Q9BXP5 | protein_coding | deleterious(0) | possibly_damaging(0.544) | TCGA-AR-A24Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| SRRT | SNV | Missense_Mutation | novel | c.456N>G | p.Phe152Leu | p.F152L | Q9BXP5 | protein_coding | tolerated(0.38) | probably_damaging(0.973) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SRRT | SNV | Missense_Mutation | rs199528372 | c.2242N>A | p.Ala748Thr | p.A748T | Q9BXP5 | protein_coding | tolerated(0.36) | benign(0.041) | TCGA-E9-A22H-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| SRRT | insertion | Frame_Shift_Ins | novel | c.800_801insATCCC | p.Leu268SerfsTer30 | p.L268Sfs*30 | Q9BXP5 | protein_coding | TCGA-A8-A08T-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| SRRT | SNV | Missense_Mutation | c.118N>A | p.Asp40Asn | p.D40N | Q9BXP5 | protein_coding | deleterious(0.05) | benign(0.227) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| SRRT | SNV | Missense_Mutation | c.2230N>G | p.Lys744Glu | p.K744E | Q9BXP5 | protein_coding | tolerated(0.05) | possibly_damaging(0.85) | TCGA-C5-A1M6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| SRRT | SNV | Missense_Mutation | c.2594G>A | p.Arg865Gln | p.R865Q | Q9BXP5 | protein_coding | deleterious(0.01) | probably_damaging(0.953) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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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