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Gene: EDEM3 |
Gene summary for EDEM3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | EDEM3 | Gene ID | 80267 |
| Gene name | ER degradation enhancing alpha-mannosidase like protein 3 | |
| Gene Alias | C1orf22 | |
| Cytomap | 1q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | Q9BZQ6 |
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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 |
| 80267 | EDEM3 | LZE4T | Human | Esophagus | ESCC | 4.43e-14 | 2.85e-01 | 0.0811 |
| 80267 | EDEM3 | LZE7T | Human | Esophagus | ESCC | 5.64e-12 | 5.23e-01 | 0.0667 |
| 80267 | EDEM3 | LZE8T | Human | Esophagus | ESCC | 6.74e-04 | 1.65e-01 | 0.067 |
| 80267 | EDEM3 | LZE20T | Human | Esophagus | ESCC | 5.45e-03 | 1.39e-01 | 0.0662 |
| 80267 | EDEM3 | LZE22T | Human | Esophagus | ESCC | 4.44e-03 | 3.72e-01 | 0.068 |
| 80267 | EDEM3 | LZE24T | Human | Esophagus | ESCC | 8.45e-11 | 3.23e-01 | 0.0596 |
| 80267 | EDEM3 | LZE21T | Human | Esophagus | ESCC | 2.08e-03 | 2.31e-01 | 0.0655 |
| 80267 | EDEM3 | P1T-E | Human | Esophagus | ESCC | 1.86e-09 | 3.30e-01 | 0.0875 |
| 80267 | EDEM3 | P2T-E | Human | Esophagus | ESCC | 2.72e-26 | 3.79e-01 | 0.1177 |
| 80267 | EDEM3 | P4T-E | Human | Esophagus | ESCC | 2.42e-23 | 4.76e-01 | 0.1323 |
| 80267 | EDEM3 | P5T-E | Human | Esophagus | ESCC | 1.92e-11 | 2.42e-01 | 0.1327 |
| 80267 | EDEM3 | P8T-E | Human | Esophagus | ESCC | 7.51e-22 | 3.08e-01 | 0.0889 |
| 80267 | EDEM3 | P9T-E | Human | Esophagus | ESCC | 1.27e-17 | 4.21e-01 | 0.1131 |
| 80267 | EDEM3 | P10T-E | Human | Esophagus | ESCC | 7.63e-32 | 5.23e-01 | 0.116 |
| 80267 | EDEM3 | P11T-E | Human | Esophagus | ESCC | 2.36e-12 | 3.20e-01 | 0.1426 |
| 80267 | EDEM3 | P12T-E | Human | Esophagus | ESCC | 4.71e-18 | 2.74e-01 | 0.1122 |
| 80267 | EDEM3 | P15T-E | Human | Esophagus | ESCC | 6.19e-22 | 4.30e-01 | 0.1149 |
| 80267 | EDEM3 | P16T-E | Human | Esophagus | ESCC | 1.28e-25 | 4.23e-01 | 0.1153 |
| 80267 | EDEM3 | P19T-E | Human | Esophagus | ESCC | 2.95e-03 | 2.45e-01 | 0.1662 |
| 80267 | EDEM3 | P20T-E | Human | Esophagus | ESCC | 8.62e-12 | 3.59e-01 | 0.1124 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:004316118 | Prostate | BPH | proteasome-mediated ubiquitin-dependent protein catabolic process | 127/3107 | 412/18723 | 3.84e-13 | 3.60e-11 | 127 |
| GO:00365034 | Prostate | BPH | ERAD pathway | 35/3107 | 107/18723 | 3.17e-05 | 3.60e-04 | 35 |
| GO:00304333 | Prostate | BPH | ubiquitin-dependent ERAD pathway | 29/3107 | 85/18723 | 6.22e-05 | 6.23e-04 | 29 |
| GO:001049819 | Prostate | Tumor | proteasomal protein catabolic process | 158/3246 | 490/18723 | 3.05e-16 | 6.76e-14 | 158 |
| GO:000698619 | Prostate | Tumor | response to unfolded protein | 65/3246 | 137/18723 | 3.56e-16 | 7.50e-14 | 65 |
| GO:003497619 | Prostate | Tumor | response to endoplasmic reticulum stress | 97/3246 | 256/18723 | 2.92e-15 | 4.78e-13 | 97 |
| GO:003596619 | Prostate | Tumor | response to topologically incorrect protein | 69/3246 | 159/18723 | 1.28e-14 | 1.81e-12 | 69 |
| GO:004316119 | Prostate | Tumor | proteasome-mediated ubiquitin-dependent protein catabolic process | 130/3246 | 412/18723 | 7.97e-13 | 8.00e-11 | 130 |
| GO:003043312 | Prostate | Tumor | ubiquitin-dependent ERAD pathway | 30/3246 | 85/18723 | 5.26e-05 | 5.75e-04 | 30 |
| GO:003650313 | Prostate | Tumor | ERAD pathway | 35/3246 | 107/18723 | 8.02e-05 | 8.19e-04 | 35 |
| GO:0010498113 | Thyroid | PTC | proteasomal protein catabolic process | 297/5968 | 490/18723 | 4.58e-40 | 9.63e-37 | 297 |
| GO:0043161113 | Thyroid | PTC | proteasome-mediated ubiquitin-dependent protein catabolic process | 254/5968 | 412/18723 | 3.91e-36 | 4.54e-33 | 254 |
| GO:0034976113 | Thyroid | PTC | response to endoplasmic reticulum stress | 161/5968 | 256/18723 | 1.14e-24 | 3.27e-22 | 161 |
| GO:0035966113 | Thyroid | PTC | response to topologically incorrect protein | 101/5968 | 159/18723 | 2.00e-16 | 1.66e-14 | 101 |
| GO:0006986113 | Thyroid | PTC | response to unfolded protein | 87/5968 | 137/18723 | 2.46e-14 | 1.57e-12 | 87 |
| GO:00365038 | Thyroid | PTC | ERAD pathway | 71/5968 | 107/18723 | 2.37e-13 | 1.22e-11 | 71 |
| GO:003043315 | Thyroid | PTC | ubiquitin-dependent ERAD pathway | 59/5968 | 85/18723 | 1.30e-12 | 5.91e-11 | 59 |
| GO:00064866 | Thyroid | PTC | protein glycosylation | 94/5968 | 226/18723 | 1.25e-03 | 7.13e-03 | 94 |
| GO:00434136 | Thyroid | PTC | macromolecule glycosylation | 94/5968 | 226/18723 | 1.25e-03 | 7.13e-03 | 94 |
| GO:00700855 | Thyroid | PTC | glycosylation | 96/5968 | 240/18723 | 4.57e-03 | 2.15e-02 | 96 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04141211 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
| hsa04141310 | Esophagus | ESCC | Protein processing in endoplasmic reticulum | 147/4205 | 174/8465 | 3.29e-22 | 1.10e-19 | 5.64e-20 | 147 |
| hsa0414122 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
| hsa0414132 | Liver | HCC | Protein processing in endoplasmic reticulum | 146/4020 | 174/8465 | 7.34e-24 | 2.46e-21 | 1.37e-21 | 146 |
| hsa0414128 | Prostate | BPH | Protein processing in endoplasmic reticulum | 97/1718 | 174/8465 | 2.37e-25 | 1.30e-23 | 8.07e-24 | 97 |
| hsa04141112 | Prostate | BPH | Protein processing in endoplasmic reticulum | 97/1718 | 174/8465 | 2.37e-25 | 1.30e-23 | 8.07e-24 | 97 |
| hsa0414129 | Prostate | Tumor | Protein processing in endoplasmic reticulum | 99/1791 | 174/8465 | 2.58e-25 | 1.71e-23 | 1.06e-23 | 99 |
| hsa0414137 | Prostate | Tumor | Protein processing in endoplasmic reticulum | 99/1791 | 174/8465 | 2.58e-25 | 1.71e-23 | 1.06e-23 | 99 |
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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 |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720T>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-A2-A1FW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720N>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-A2-A1G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720T>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-A2-A1G4-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | adriamycin | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720T>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| EDEM3 | SNV | Missense_Mutation | rs745987472 | c.1943N>A | p.Arg648Gln | p.R648Q | Q9BZQ6 | protein_coding | tolerated(0.27) | benign(0.079) | TCGA-A7-A26E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720T>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-A8-A06R-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| EDEM3 | SNV | Missense_Mutation | novel | c.391T>G | p.Leu131Val | p.L131V | Q9BZQ6 | protein_coding | tolerated(0.64) | benign(0.001) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720T>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-AO-A1KP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720N>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-AQ-A1H3-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| EDEM3 | SNV | Missense_Mutation | rs201554031 | c.2720N>C | p.Val907Ala | p.V907A | Q9BZQ6 | protein_coding | tolerated_low_confidence(0.77) | benign(0) | TCGA-AR-A1AP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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