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Gene: EDEM1 |
Gene summary for EDEM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | EDEM1 | Gene ID | 9695 |
| Gene name | ER degradation enhancing alpha-mannosidase like protein 1 | |
| Gene Alias | EDEM | |
| Cytomap | 3p26.1 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | A0A024R2D5 |
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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 |
| 9695 | EDEM1 | NAFLD1 | Human | Liver | NAFLD | 3.45e-05 | 4.80e-01 | -0.04 |
| 9695 | EDEM1 | S43 | Human | Liver | Cirrhotic | 5.09e-03 | 2.25e-02 | -0.0187 |
| 9695 | EDEM1 | HCC1_Meng | Human | Liver | HCC | 7.74e-39 | 2.63e-02 | 0.0246 |
| 9695 | EDEM1 | HCC2_Meng | Human | Liver | HCC | 5.15e-03 | -7.52e-02 | 0.0107 |
| 9695 | EDEM1 | HCC2 | Human | Liver | HCC | 6.31e-07 | 2.70e+00 | 0.5341 |
| 9695 | EDEM1 | S015 | Human | Liver | HCC | 1.59e-02 | 2.98e-01 | 0.2375 |
| 9695 | EDEM1 | S027 | Human | Liver | HCC | 2.79e-07 | 7.16e-01 | 0.2446 |
| 9695 | EDEM1 | S028 | Human | Liver | HCC | 8.50e-22 | 9.57e-01 | 0.2503 |
| 9695 | EDEM1 | S029 | Human | Liver | HCC | 1.74e-18 | 9.00e-01 | 0.2581 |
| 9695 | EDEM1 | C21 | Human | Oral cavity | OSCC | 1.11e-04 | 2.13e-01 | 0.2678 |
| 9695 | EDEM1 | C30 | Human | Oral cavity | OSCC | 3.23e-23 | 9.16e-01 | 0.3055 |
| 9695 | EDEM1 | C51 | Human | Oral cavity | OSCC | 1.81e-12 | 4.31e-01 | 0.2674 |
| 9695 | EDEM1 | C57 | Human | Oral cavity | OSCC | 1.30e-15 | 5.51e-01 | 0.1679 |
| 9695 | EDEM1 | C08 | Human | Oral cavity | OSCC | 6.29e-04 | 1.28e-01 | 0.1919 |
| 9695 | EDEM1 | C09 | Human | Oral cavity | OSCC | 1.36e-02 | 1.40e-01 | 0.1431 |
| 9695 | EDEM1 | LN46 | Human | Oral cavity | OSCC | 2.03e-04 | 2.00e-01 | 0.1666 |
| 9695 | EDEM1 | EOLP-1 | Human | Oral cavity | EOLP | 4.13e-06 | 3.31e-01 | -0.0202 |
| 9695 | EDEM1 | SYSMH1 | Human | Oral cavity | OSCC | 1.24e-02 | 1.25e-01 | 0.1127 |
| 9695 | EDEM1 | SYSMH3 | Human | Oral cavity | OSCC | 2.54e-07 | 2.44e-01 | 0.2442 |
| 9695 | EDEM1 | SYSMH6 | Human | Oral cavity | OSCC | 4.61e-06 | 9.86e-02 | 0.1275 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:003238818 | Oral cavity | OSCC | positive regulation of intracellular transport | 134/7305 | 202/18723 | 2.82e-15 | 1.88e-13 | 134 |
| GO:009031610 | Oral cavity | OSCC | positive regulation of intracellular protein transport | 110/7305 | 160/18723 | 2.10e-14 | 1.19e-12 | 110 |
| GO:00304334 | Oral cavity | OSCC | ubiquitin-dependent ERAD pathway | 65/7305 | 85/18723 | 2.12e-12 | 8.99e-11 | 65 |
| GO:00365035 | Oral cavity | OSCC | ERAD pathway | 76/7305 | 107/18723 | 1.76e-11 | 6.11e-10 | 76 |
| GO:00325276 | Oral cavity | OSCC | protein exit from endoplasmic reticulum | 36/7305 | 48/18723 | 4.31e-07 | 6.36e-06 | 36 |
| GO:00709729 | Oral cavity | OSCC | protein localization to endoplasmic reticulum | 50/7305 | 74/18723 | 6.03e-07 | 8.64e-06 | 50 |
| GO:00309705 | Oral cavity | OSCC | retrograde protein transport, ER to cytosol | 23/7305 | 29/18723 | 1.13e-05 | 1.16e-04 | 23 |
| GO:19035135 | Oral cavity | OSCC | endoplasmic reticulum to cytosol transport | 23/7305 | 29/18723 | 1.13e-05 | 1.16e-04 | 23 |
| GO:00708614 | Oral cavity | OSCC | regulation of protein exit from endoplasmic reticulum | 20/7305 | 27/18723 | 2.32e-04 | 1.51e-03 | 20 |
| GO:00091001 | Oral cavity | OSCC | glycoprotein metabolic process | 185/7305 | 387/18723 | 2.37e-04 | 1.54e-03 | 185 |
| GO:00725998 | Oral cavity | OSCC | establishment of protein localization to endoplasmic reticulum | 30/7305 | 46/18723 | 2.86e-04 | 1.80e-03 | 30 |
| GO:19011361 | Oral cavity | OSCC | carbohydrate derivative catabolic process | 89/7305 | 172/18723 | 4.52e-04 | 2.73e-03 | 89 |
| GO:00450477 | Oral cavity | OSCC | protein targeting to ER | 27/7305 | 42/18723 | 8.00e-04 | 4.29e-03 | 27 |
| GO:19041523 | Oral cavity | OSCC | regulation of retrograde protein transport, ER to cytosol | 11/7305 | 14/18723 | 3.09e-03 | 1.33e-02 | 11 |
| GO:007259425 | Oral cavity | EOLP | establishment of protein localization to organelle | 108/2218 | 422/18723 | 2.91e-15 | 1.45e-12 | 108 |
| GO:003238622 | Oral cavity | EOLP | regulation of intracellular transport | 91/2218 | 337/18723 | 1.51e-14 | 6.47e-12 | 91 |
| GO:003596624 | Oral cavity | EOLP | response to topologically incorrect protein | 54/2218 | 159/18723 | 1.93e-13 | 6.44e-11 | 54 |
| GO:000698624 | Oral cavity | EOLP | response to unfolded protein | 48/2218 | 137/18723 | 1.14e-12 | 2.52e-10 | 48 |
| GO:003315722 | Oral cavity | EOLP | regulation of intracellular protein transport | 63/2218 | 229/18723 | 7.28e-11 | 9.09e-09 | 63 |
| GO:001049825 | Oral cavity | EOLP | proteasomal protein catabolic process | 108/2218 | 490/18723 | 7.79e-11 | 9.51e-09 | 108 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414114 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
| hsa0414115 | Liver | Cirrhotic | Protein processing in endoplasmic reticulum | 114/2530 | 174/8465 | 1.16e-22 | 9.67e-21 | 5.96e-21 | 114 |
| 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 |
| hsa0414130 | Oral cavity | OSCC | Protein processing in endoplasmic reticulum | 143/3704 | 174/8465 | 6.82e-26 | 2.28e-23 | 1.16e-23 | 143 |
| hsa04141113 | Oral cavity | OSCC | Protein processing in endoplasmic reticulum | 143/3704 | 174/8465 | 6.82e-26 | 2.28e-23 | 1.16e-23 | 143 |
| hsa0414145 | Oral cavity | EOLP | Protein processing in endoplasmic reticulum | 70/1218 | 174/8465 | 2.84e-17 | 3.06e-15 | 1.81e-15 | 70 |
| hsa0414155 | Oral cavity | EOLP | Protein processing in endoplasmic reticulum | 70/1218 | 174/8465 | 2.84e-17 | 3.06e-15 | 1.81e-15 | 70 |
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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 |
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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 |
| EDEM1 | SNV | Missense_Mutation | c.1607N>G | p.His536Arg | p.H536R | Q92611 | protein_coding | deleterious(0.03) | possibly_damaging(0.636) | TCGA-A8-A08J-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| EDEM1 | SNV | Missense_Mutation | c.775N>A | p.Glu259Lys | p.E259K | Q92611 | protein_coding | deleterious(0.01) | benign(0.213) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| EDEM1 | SNV | Missense_Mutation | c.1643N>C | p.Ser548Thr | p.S548T | Q92611 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-AR-A1AO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| EDEM1 | SNV | Missense_Mutation | c.1527N>G | p.Phe509Leu | p.F509L | Q92611 | protein_coding | deleterious(0.01) | possibly_damaging(0.876) | TCGA-C5-A1M6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| EDEM1 | SNV | Missense_Mutation | c.85C>T | p.Pro29Ser | p.P29S | Q92611 | protein_coding | deleterious_low_confidence(0.02) | benign(0.037) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| EDEM1 | SNV | Missense_Mutation | c.791N>G | p.Ala264Gly | p.A264G | Q92611 | protein_coding | deleterious(0.01) | probably_damaging(0.992) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| EDEM1 | SNV | Missense_Mutation | c.1700C>A | p.Pro567Gln | p.P567Q | Q92611 | protein_coding | deleterious(0.01) | probably_damaging(0.969) | TCGA-AA-A01Z-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| EDEM1 | SNV | Missense_Mutation | novel | c.1193N>T | p.Ser398Ile | p.S398I | Q92611 | protein_coding | deleterious(0.01) | possibly_damaging(0.781) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| EDEM1 | SNV | Missense_Mutation | novel | c.1211N>T | p.Arg404Ile | p.R404I | Q92611 | protein_coding | deleterious(0) | possibly_damaging(0.886) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| EDEM1 | SNV | Missense_Mutation | c.817N>G | p.Pro273Ala | p.P273A | Q92611 | protein_coding | deleterious(0) | probably_damaging(0.933) | TCGA-CK-5912-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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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 |
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