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Gene: EDC3 |
Gene summary for EDC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | EDC3 | Gene ID | 80153 |
| Gene name | enhancer of mRNA decapping 3 | |
| Gene Alias | LSM16 | |
| Cytomap | 15q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0000956 | UniProtAcc | Q96F86 |
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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 |
| 80153 | EDC3 | LZE4T | Human | Esophagus | ESCC | 1.03e-04 | 1.92e-01 | 0.0811 |
| 80153 | EDC3 | LZE7T | Human | Esophagus | ESCC | 2.54e-05 | 3.43e-01 | 0.0667 |
| 80153 | EDC3 | LZE24T | Human | Esophagus | ESCC | 4.76e-05 | 1.02e-01 | 0.0596 |
| 80153 | EDC3 | P1T-E | Human | Esophagus | ESCC | 7.56e-05 | 2.73e-01 | 0.0875 |
| 80153 | EDC3 | P2T-E | Human | Esophagus | ESCC | 8.34e-20 | 2.76e-01 | 0.1177 |
| 80153 | EDC3 | P4T-E | Human | Esophagus | ESCC | 8.44e-17 | 3.40e-01 | 0.1323 |
| 80153 | EDC3 | P5T-E | Human | Esophagus | ESCC | 1.74e-04 | 9.92e-02 | 0.1327 |
| 80153 | EDC3 | P8T-E | Human | Esophagus | ESCC | 7.77e-14 | 2.08e-01 | 0.0889 |
| 80153 | EDC3 | P9T-E | Human | Esophagus | ESCC | 1.75e-09 | 1.68e-01 | 0.1131 |
| 80153 | EDC3 | P10T-E | Human | Esophagus | ESCC | 3.51e-16 | 2.44e-01 | 0.116 |
| 80153 | EDC3 | P11T-E | Human | Esophagus | ESCC | 4.21e-09 | 2.81e-01 | 0.1426 |
| 80153 | EDC3 | P12T-E | Human | Esophagus | ESCC | 8.60e-18 | 2.89e-01 | 0.1122 |
| 80153 | EDC3 | P15T-E | Human | Esophagus | ESCC | 1.76e-16 | 2.80e-01 | 0.1149 |
| 80153 | EDC3 | P16T-E | Human | Esophagus | ESCC | 1.67e-14 | 3.97e-01 | 0.1153 |
| 80153 | EDC3 | P17T-E | Human | Esophagus | ESCC | 1.87e-04 | 2.13e-01 | 0.1278 |
| 80153 | EDC3 | P20T-E | Human | Esophagus | ESCC | 2.28e-09 | 1.37e-01 | 0.1124 |
| 80153 | EDC3 | P21T-E | Human | Esophagus | ESCC | 4.03e-19 | 1.69e-01 | 0.1617 |
| 80153 | EDC3 | P22T-E | Human | Esophagus | ESCC | 3.16e-15 | 2.05e-01 | 0.1236 |
| 80153 | EDC3 | P23T-E | Human | Esophagus | ESCC | 4.20e-12 | 2.56e-01 | 0.108 |
| 80153 | EDC3 | P24T-E | Human | Esophagus | ESCC | 6.57e-10 | 1.15e-01 | 0.1287 |
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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 |
| ∗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:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:0006402110 | Esophagus | ESCC | mRNA catabolic process | 170/8552 | 232/18723 | 8.70e-18 | 8.00e-16 | 170 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:000095618 | Esophagus | ESCC | nuclear-transcribed mRNA catabolic process | 88/8552 | 112/18723 | 9.41e-13 | 4.14e-11 | 88 |
| GO:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
| GO:003396214 | Esophagus | ESCC | P-body assembly | 16/8552 | 21/18723 | 4.47e-03 | 1.76e-02 | 16 |
| GO:0110154 | Esophagus | ESCC | RNA decapping | 14/8552 | 18/18723 | 5.77e-03 | 2.14e-02 | 14 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301824 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| hsa0301834 | Esophagus | ESCC | RNA degradation | 62/4205 | 79/8465 | 1.18e-07 | 9.39e-07 | 4.81e-07 | 62 |
| 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 |
| EDC3 | SNV | Missense_Mutation | c.664N>G | p.Ile222Val | p.I222V | Q96F86 | protein_coding | deleterious(0.01) | benign(0.007) | TCGA-BH-A0WA-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| EDC3 | SNV | Missense_Mutation | c.613N>C | p.Asp205His | p.D205H | Q96F86 | protein_coding | deleterious(0) | probably_damaging(0.957) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| EDC3 | SNV | Missense_Mutation | c.343N>G | p.Gln115Glu | p.Q115E | Q96F86 | protein_coding | tolerated(0.56) | benign(0.071) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| EDC3 | SNV | Missense_Mutation | c.622G>A | p.Gly208Arg | p.G208R | Q96F86 | protein_coding | tolerated(0.08) | benign(0.046) | TCGA-DS-A0VM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| EDC3 | SNV | Missense_Mutation | rs772170307 | c.776N>A | p.Arg259Gln | p.R259Q | Q96F86 | protein_coding | tolerated(0.1) | possibly_damaging(0.604) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| EDC3 | deletion | Frame_Shift_Del | c.1042delN | p.Ala348LeufsTer10 | p.A348Lfs*10 | Q96F86 | protein_coding | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |||
| EDC3 | SNV | Missense_Mutation | c.961G>A | p.Gly321Arg | p.G321R | Q96F86 | protein_coding | deleterious(0) | probably_damaging(0.939) | TCGA-AU-3779-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| EDC3 | SNV | Missense_Mutation | novel | c.375N>G | p.Ser125Arg | p.S125R | Q96F86 | protein_coding | tolerated(0.68) | benign(0.02) | TCGA-AY-4070-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | 5-fu | PD |
| EDC3 | SNV | Missense_Mutation | novel | c.189N>C | p.Lys63Asn | p.K63N | Q96F86 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| EDC3 | deletion | Frame_Shift_Del | c.1042delG | p.Ala348LeufsTer10 | p.A348Lfs*10 | Q96F86 | protein_coding | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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