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Gene: REST |
Gene summary for REST |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | REST | Gene ID | 5978 |
| Gene name | RE1 silencing transcription factor | |
| Gene Alias | DFNA27 | |
| Cytomap | 4q12 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q13127 |
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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 |
| 5978 | REST | LZE2T | Human | Esophagus | ESCC | 1.52e-02 | 5.83e-01 | 0.082 |
| 5978 | REST | LZE4T | Human | Esophagus | ESCC | 5.92e-15 | 4.81e-01 | 0.0811 |
| 5978 | REST | LZE5T | Human | Esophagus | ESCC | 5.23e-03 | 2.24e-01 | 0.0514 |
| 5978 | REST | LZE7T | Human | Esophagus | ESCC | 2.65e-04 | 3.94e-01 | 0.0667 |
| 5978 | REST | LZE8T | Human | Esophagus | ESCC | 8.02e-06 | 1.11e-01 | 0.067 |
| 5978 | REST | LZE20T | Human | Esophagus | ESCC | 7.39e-08 | 2.78e-01 | 0.0662 |
| 5978 | REST | LZE21D1 | Human | Esophagus | HGIN | 4.54e-02 | 1.16e-01 | 0.0632 |
| 5978 | REST | LZE22T | Human | Esophagus | ESCC | 5.18e-04 | 4.03e-01 | 0.068 |
| 5978 | REST | LZE24T | Human | Esophagus | ESCC | 6.48e-25 | 7.52e-01 | 0.0596 |
| 5978 | REST | LZE21T | Human | Esophagus | ESCC | 3.53e-08 | 4.36e-01 | 0.0655 |
| 5978 | REST | P1T-E | Human | Esophagus | ESCC | 9.93e-14 | 7.14e-01 | 0.0875 |
| 5978 | REST | P2T-E | Human | Esophagus | ESCC | 5.17e-82 | 1.40e+00 | 0.1177 |
| 5978 | REST | P4T-E | Human | Esophagus | ESCC | 1.20e-43 | 9.93e-01 | 0.1323 |
| 5978 | REST | P5T-E | Human | Esophagus | ESCC | 1.10e-21 | 4.16e-01 | 0.1327 |
| 5978 | REST | P8T-E | Human | Esophagus | ESCC | 3.71e-50 | 1.01e+00 | 0.0889 |
| 5978 | REST | P9T-E | Human | Esophagus | ESCC | 5.27e-16 | 3.83e-01 | 0.1131 |
| 5978 | REST | P10T-E | Human | Esophagus | ESCC | 4.10e-50 | 8.64e-01 | 0.116 |
| 5978 | REST | P11T-E | Human | Esophagus | ESCC | 2.58e-14 | 6.56e-01 | 0.1426 |
| 5978 | REST | P12T-E | Human | Esophagus | ESCC | 1.08e-47 | 1.09e+00 | 0.1122 |
| 5978 | REST | P15T-E | Human | Esophagus | ESCC | 1.98e-46 | 9.90e-01 | 0.1149 |
| Page: 1 2 3 4 5 6 7 8 |
| 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:19032049 | Prostate | BPH | negative regulation of oxidative stress-induced neuron death | 10/3107 | 19/18723 | 3.36e-04 | 2.52e-03 | 10 |
| GO:190040716 | Prostate | BPH | regulation of cellular response to oxidative stress | 28/3107 | 89/18723 | 3.90e-04 | 2.85e-03 | 28 |
| GO:190288216 | Prostate | BPH | regulation of response to oxidative stress | 30/3107 | 98/18723 | 4.16e-04 | 3.01e-03 | 30 |
| GO:00620127 | Prostate | BPH | regulation of small molecule metabolic process | 79/3107 | 334/18723 | 5.17e-04 | 3.66e-03 | 79 |
| GO:00519604 | Prostate | BPH | regulation of nervous system development | 100/3107 | 443/18723 | 6.02e-04 | 4.16e-03 | 100 |
| GO:19012158 | Prostate | BPH | negative regulation of neuron death | 53/3107 | 208/18723 | 6.87e-04 | 4.58e-03 | 53 |
| GO:00356013 | Prostate | BPH | protein deacylation | 32/3107 | 112/18723 | 1.03e-03 | 6.46e-03 | 32 |
| GO:00060816 | Prostate | BPH | cellular aldehyde metabolic process | 20/3107 | 60/18723 | 1.14e-03 | 7.10e-03 | 20 |
| GO:00064763 | Prostate | BPH | protein deacetylation | 29/3107 | 101/18723 | 1.59e-03 | 9.28e-03 | 29 |
| GO:00987323 | Prostate | BPH | macromolecule deacylation | 32/3107 | 116/18723 | 1.94e-03 | 1.10e-02 | 32 |
| GO:00107214 | Prostate | BPH | negative regulation of cell development | 45/3107 | 180/18723 | 2.49e-03 | 1.34e-02 | 45 |
| GO:0035051 | Prostate | BPH | cardiocyte differentiation | 40/3107 | 156/18723 | 2.58e-03 | 1.38e-02 | 40 |
| GO:00716928 | Prostate | BPH | protein localization to extracellular region | 82/3107 | 368/18723 | 2.59e-03 | 1.39e-02 | 82 |
| GO:00093069 | Prostate | BPH | protein secretion | 80/3107 | 359/18723 | 2.89e-03 | 1.52e-02 | 80 |
| GO:00518516 | Prostate | BPH | modulation by host of symbiont process | 19/3107 | 60/18723 | 2.94e-03 | 1.54e-02 | 19 |
| GO:00355929 | Prostate | BPH | establishment of protein localization to extracellular region | 80/3107 | 360/18723 | 3.13e-03 | 1.63e-02 | 80 |
| GO:00507088 | Prostate | BPH | regulation of protein secretion | 62/3107 | 268/18723 | 3.35e-03 | 1.73e-02 | 62 |
| GO:190320210 | Prostate | BPH | negative regulation of oxidative stress-induced cell death | 17/3107 | 53/18723 | 4.11e-03 | 2.04e-02 | 17 |
| GO:00454452 | Prostate | BPH | myoblast differentiation | 24/3107 | 84/18723 | 4.13e-03 | 2.04e-02 | 24 |
| GO:19032093 | Prostate | BPH | positive regulation of oxidative stress-induced cell death | 8/3107 | 18/18723 | 5.17e-03 | 2.43e-02 | 8 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501630 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa05016113 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa0501638 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa0501614 | Liver | Cirrhotic | Huntington disease | 172/2530 | 306/8465 | 1.65e-22 | 1.10e-20 | 6.77e-21 | 172 |
| hsa0501615 | Liver | Cirrhotic | Huntington disease | 172/2530 | 306/8465 | 1.65e-22 | 1.10e-20 | 6.77e-21 | 172 |
| hsa0501622 | Liver | HCC | Huntington disease | 219/4020 | 306/8465 | 3.06e-18 | 3.42e-16 | 1.90e-16 | 219 |
| hsa0501632 | Liver | HCC | Huntington disease | 219/4020 | 306/8465 | 3.06e-18 | 3.42e-16 | 1.90e-16 | 219 |
| hsa0501628 | Oral cavity | OSCC | Huntington disease | 204/3704 | 306/8465 | 1.70e-16 | 7.13e-15 | 3.63e-15 | 204 |
| hsa05016112 | Oral cavity | OSCC | Huntington disease | 204/3704 | 306/8465 | 1.70e-16 | 7.13e-15 | 3.63e-15 | 204 |
| hsa0501626 | Prostate | BPH | Huntington disease | 149/1718 | 306/8465 | 8.82e-30 | 7.27e-28 | 4.50e-28 | 149 |
| hsa05016111 | Prostate | BPH | Huntington disease | 149/1718 | 306/8465 | 8.82e-30 | 7.27e-28 | 4.50e-28 | 149 |
| hsa0501627 | Prostate | Tumor | Huntington disease | 150/1791 | 306/8465 | 2.72e-28 | 2.25e-26 | 1.40e-26 | 150 |
| hsa0501636 | Prostate | Tumor | Huntington disease | 150/1791 | 306/8465 | 2.72e-28 | 2.25e-26 | 1.40e-26 | 150 |
| 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 |
| REST | MAIT | Colorectum | SER | MTHFR,PSD3,SPECC1, etc. | 2.66e-02 |  |
| REST | STM | Oral cavity | LP | GABRP,FAM111B,RP11-983G14.1, etc. | 5.24e-01 |  |
| ∗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 |
| REST | SNV | Missense_Mutation | c.3189N>G | p.Ile1063Met | p.I1063M | Q13127 | protein_coding | deleterious(0) | probably_damaging(0.946) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| REST | SNV | Missense_Mutation | novel | c.622N>A | p.Glu208Lys | p.E208K | Q13127 | protein_coding | tolerated(0.19) | probably_damaging(0.993) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| REST | SNV | Missense_Mutation | c.1114G>C | p.Asp372His | p.D372H | Q13127 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| REST | SNV | Missense_Mutation | c.2746N>A | p.Ser916Thr | p.S916T | Q13127 | protein_coding | tolerated(0.13) | benign(0.257) | TCGA-E9-A1R7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | fareston | SD | |
| REST | insertion | Nonsense_Mutation | novel | c.662_663insAGCACCCTTCCCCTCC | p.Cys221Ter | p.C221* | Q13127 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| REST | insertion | Frame_Shift_Ins | novel | c.664_665insCAGATGATCCTGGAGT | p.Gly222AlafsTer10 | p.G222Afs*10 | Q13127 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| REST | insertion | Frame_Shift_Ins | novel | c.3029_3030insAGCCTGCT | p.Ile1011AlafsTer12 | p.I1011Afs*12 | Q13127 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| REST | insertion | In_Frame_Ins | novel | c.3031_3032insGAGGGAGCCACCTCC | p.Ile1011delinsArgGlySerHisLeuLeu | p.I1011delinsRGSHLL | Q13127 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| REST | insertion | Nonsense_Mutation | novel | c.3204_3205insGAAATTTAGGGTGGAGGGAGTATGGGAATTTTA | p.Ser1068_Phe1069insGluIleTerGlyGlyGlySerMetGlyIleLeu | p.S1068_F1069insEI*GGGSMGIL | Q13127 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| REST | insertion | Nonsense_Mutation | novel | c.960_961insTTGGGAGGCCAATATAGGCGGATTGCTTGAGCCC | p.Arg321LeufsTer10 | p.R321Lfs*10 | Q13127 | protein_coding | TCGA-B6-A0I8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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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