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Gene: FMR1 |
Gene summary for FMR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FMR1 | Gene ID | 2332 |
| Gene name | FMRP translational regulator 1 | |
| Gene Alias | FMRP | |
| Cytomap | Xq27.3 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q06787 |
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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 |
| 2332 | FMR1 | LZE4T | Human | Esophagus | ESCC | 8.09e-05 | 1.18e-01 | 0.0811 |
| 2332 | FMR1 | LZE7T | Human | Esophagus | ESCC | 5.27e-04 | 5.28e-01 | 0.0667 |
| 2332 | FMR1 | LZE20T | Human | Esophagus | ESCC | 1.82e-03 | 1.56e-01 | 0.0662 |
| 2332 | FMR1 | LZE24T | Human | Esophagus | ESCC | 3.58e-19 | 5.99e-01 | 0.0596 |
| 2332 | FMR1 | LZE21T | Human | Esophagus | ESCC | 1.96e-04 | 1.95e-01 | 0.0655 |
| 2332 | FMR1 | LZE6T | Human | Esophagus | ESCC | 1.36e-04 | 9.94e-02 | 0.0845 |
| 2332 | FMR1 | P1T-E | Human | Esophagus | ESCC | 1.56e-05 | 4.66e-01 | 0.0875 |
| 2332 | FMR1 | P2T-E | Human | Esophagus | ESCC | 9.72e-22 | 2.68e-01 | 0.1177 |
| 2332 | FMR1 | P4T-E | Human | Esophagus | ESCC | 3.22e-10 | 1.87e-01 | 0.1323 |
| 2332 | FMR1 | P5T-E | Human | Esophagus | ESCC | 1.14e-08 | 1.20e-01 | 0.1327 |
| 2332 | FMR1 | P8T-E | Human | Esophagus | ESCC | 7.01e-19 | 3.15e-01 | 0.0889 |
| 2332 | FMR1 | P9T-E | Human | Esophagus | ESCC | 1.05e-12 | 2.97e-01 | 0.1131 |
| 2332 | FMR1 | P10T-E | Human | Esophagus | ESCC | 1.22e-26 | 4.39e-01 | 0.116 |
| 2332 | FMR1 | P11T-E | Human | Esophagus | ESCC | 2.25e-05 | 1.61e-01 | 0.1426 |
| 2332 | FMR1 | P12T-E | Human | Esophagus | ESCC | 5.34e-19 | 2.77e-01 | 0.1122 |
| 2332 | FMR1 | P15T-E | Human | Esophagus | ESCC | 4.91e-19 | 2.11e-01 | 0.1149 |
| 2332 | FMR1 | P16T-E | Human | Esophagus | ESCC | 2.42e-06 | 4.91e-02 | 0.1153 |
| 2332 | FMR1 | P19T-E | Human | Esophagus | ESCC | 1.00e-05 | 3.58e-01 | 0.1662 |
| 2332 | FMR1 | P20T-E | Human | Esophagus | ESCC | 7.18e-05 | 1.80e-01 | 0.1124 |
| 2332 | FMR1 | P21T-E | Human | Esophagus | ESCC | 3.06e-09 | 2.06e-01 | 0.1617 |
| 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. |
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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:005109822 | Liver | HCC | regulation of binding | 225/7958 | 363/18723 | 3.78e-14 | 2.37e-12 | 225 |
| GO:005102811 | Liver | HCC | mRNA transport | 97/7958 | 130/18723 | 9.00e-14 | 5.23e-12 | 97 |
| GO:004348721 | Liver | HCC | regulation of RNA stability | 119/7958 | 170/18723 | 3.20e-13 | 1.71e-11 | 119 |
| GO:004440322 | Liver | HCC | biological process involved in symbiotic interaction | 183/7958 | 290/18723 | 9.13e-13 | 4.59e-11 | 183 |
| GO:190305221 | Liver | HCC | positive regulation of proteolysis involved in cellular protein catabolic process | 96/7958 | 133/18723 | 3.47e-12 | 1.57e-10 | 96 |
| GO:004348821 | Liver | HCC | regulation of mRNA stability | 110/7958 | 158/18723 | 4.36e-12 | 1.93e-10 | 110 |
| GO:006101321 | Liver | HCC | regulation of mRNA catabolic process | 114/7958 | 166/18723 | 7.38e-12 | 3.12e-10 | 114 |
| GO:000989522 | Liver | HCC | negative regulation of catabolic process | 196/7958 | 320/18723 | 7.98e-12 | 3.35e-10 | 196 |
| GO:004572712 | Liver | HCC | positive regulation of translation | 97/7958 | 136/18723 | 8.51e-12 | 3.55e-10 | 97 |
| GO:001907922 | Liver | HCC | viral genome replication | 94/7958 | 131/18723 | 1.02e-11 | 4.18e-10 | 94 |
| GO:190180012 | Liver | HCC | positive regulation of proteasomal protein catabolic process | 84/7958 | 114/18723 | 1.28e-11 | 5.21e-10 | 84 |
| GO:003133022 | Liver | HCC | negative regulation of cellular catabolic process | 164/7958 | 262/18723 | 3.52e-11 | 1.35e-09 | 164 |
| GO:003425022 | Liver | HCC | positive regulation of cellular amide metabolic process | 110/7958 | 162/18723 | 5.14e-11 | 1.92e-09 | 110 |
| GO:000644622 | Liver | HCC | regulation of translational initiation | 62/7958 | 79/18723 | 6.85e-11 | 2.48e-09 | 62 |
| GO:004802422 | Liver | HCC | regulation of mRNA splicing, via spliceosome | 74/7958 | 101/18723 | 3.29e-10 | 1.10e-08 | 74 |
| GO:005079212 | Liver | HCC | regulation of viral process | 109/7958 | 164/18723 | 4.52e-10 | 1.45e-08 | 109 |
| GO:004852411 | Liver | HCC | positive regulation of viral process | 52/7958 | 65/18723 | 6.70e-10 | 2.11e-08 | 52 |
| GO:000961511 | Liver | HCC | response to virus | 210/7958 | 367/18723 | 7.32e-09 | 1.86e-07 | 210 |
| GO:003105621 | Liver | HCC | regulation of histone modification | 99/7958 | 152/18723 | 1.40e-08 | 3.40e-07 | 99 |
| GO:005109922 | Liver | HCC | positive regulation of binding | 108/7958 | 173/18723 | 9.22e-08 | 1.83e-06 | 108 |
| 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 |
| 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 |
| FMR1 | SNV | Missense_Mutation | c.763N>G | p.Leu255Val | p.L255V | Q06787 | protein_coding | tolerated(0.08) | possibly_damaging(0.856) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD | |
| FMR1 | SNV | Missense_Mutation | novel | c.215N>C | p.Asn72Thr | p.N72T | Q06787 | protein_coding | tolerated(0.05) | probably_damaging(0.994) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD |
| FMR1 | SNV | Missense_Mutation | c.1822N>T | p.Gly608Cys | p.G608C | Q06787 | protein_coding | deleterious_low_confidence(0.02) | probably_damaging(0.935) | TCGA-A7-A56D-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| FMR1 | SNV | Missense_Mutation | rs782738200 | c.1580G>A | p.Arg527His | p.R527H | Q06787 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-B6-A401-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| FMR1 | SNV | Missense_Mutation | c.1525N>A | p.Glu509Lys | p.E509K | Q06787 | protein_coding | tolerated(0.11) | probably_damaging(0.998) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| FMR1 | SNV | Missense_Mutation | c.859N>G | p.Gln287Glu | p.Q287E | Q06787 | protein_coding | deleterious(0.03) | benign(0.214) | TCGA-C8-A12K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| FMR1 | SNV | Missense_Mutation | novel | c.283N>A | p.Glu95Lys | p.E95K | Q06787 | protein_coding | tolerated(0.09) | benign(0.03) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| FMR1 | SNV | Missense_Mutation | c.690G>T | p.Met230Ile | p.M230I | Q06787 | protein_coding | tolerated(0.05) | possibly_damaging(0.519) | TCGA-D8-A1JD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| FMR1 | SNV | Missense_Mutation | c.691G>A | p.Gly231Ser | p.G231S | Q06787 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1JD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| FMR1 | SNV | Missense_Mutation | c.1525N>A | p.Glu509Lys | p.E509K | Q06787 | protein_coding | tolerated(0.11) | probably_damaging(0.998) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| 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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