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Gene: GREM1 |
Gene summary for GREM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GREM1 | Gene ID | 26585 |
| Gene name | gremlin 1, DAN family BMP antagonist | |
| Gene Alias | C15DUPq | |
| Cytomap | 15q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | B3KTR9 |
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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 |
| 26585 | GREM1 | P4T-E | Human | Esophagus | ESCC | 1.06e-03 | 6.21e-01 | 0.1323 |
| 26585 | GREM1 | P26T-E | Human | Esophagus | ESCC | 2.00e-03 | 1.23e-02 | 0.1276 |
| 26585 | GREM1 | P44T-E | Human | Esophagus | ESCC | 6.70e-04 | 8.67e-01 | 0.1096 |
| 26585 | GREM1 | P49T-E | Human | Esophagus | ESCC | 1.34e-04 | 1.49e+00 | 0.1768 |
| 26585 | GREM1 | NEOLP-1 | Human | Oral cavity | NEOLP | 2.68e-04 | 2.30e-01 | -0.0194 |
| 26585 | GREM1 | male-WTA | Human | Thyroid | PTC | 1.68e-15 | 2.33e-01 | 0.1037 |
| 26585 | GREM1 | ATC12 | Human | Thyroid | ATC | 6.99e-29 | 7.59e-01 | 0.34 |
| 26585 | GREM1 | ATC13 | Human | Thyroid | ATC | 2.43e-03 | 1.04e-01 | 0.34 |
| 26585 | GREM1 | ATC4 | Human | Thyroid | ATC | 4.66e-35 | 9.71e-01 | 0.34 |
| 26585 | GREM1 | ATC5 | Human | Thyroid | ATC | 2.56e-04 | 1.24e-01 | 0.34 |
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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 | ||
| 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:004677722 | Oral cavity | NEOLP | protein autophosphorylation | 45/2005 | 227/18723 | 3.28e-05 | 4.87e-04 | 45 |
| GO:009028711 | Oral cavity | NEOLP | regulation of cellular response to growth factor stimulus | 56/2005 | 304/18723 | 3.55e-05 | 5.20e-04 | 56 |
| GO:009009213 | Oral cavity | NEOLP | regulation of transmembrane receptor protein serine/threonine kinase signaling pathway | 49/2005 | 256/18723 | 3.90e-05 | 5.62e-04 | 49 |
| GO:00604855 | Oral cavity | NEOLP | mesenchyme development | 54/2005 | 291/18723 | 3.95e-05 | 5.62e-04 | 54 |
| GO:004876214 | Oral cavity | NEOLP | mesenchymal cell differentiation | 46/2005 | 236/18723 | 4.18e-05 | 5.92e-04 | 46 |
| GO:005105231 | Oral cavity | NEOLP | regulation of DNA metabolic process | 63/2005 | 359/18723 | 5.48e-05 | 7.44e-04 | 63 |
| GO:000268331 | Oral cavity | NEOLP | negative regulation of immune system process | 73/2005 | 434/18723 | 6.18e-05 | 8.22e-04 | 73 |
| GO:00358506 | Oral cavity | NEOLP | epithelial cell differentiation involved in kidney development | 15/2005 | 47/18723 | 7.12e-05 | 9.27e-04 | 15 |
| GO:005105431 | Oral cavity | NEOLP | positive regulation of DNA metabolic process | 40/2005 | 201/18723 | 8.01e-05 | 1.01e-03 | 40 |
| GO:00107172 | Oral cavity | NEOLP | regulation of epithelial to mesenchymal transition | 24/2005 | 99/18723 | 9.40e-05 | 1.15e-03 | 24 |
| GO:003806131 | Oral cavity | NEOLP | NIK/NF-kappaB signaling | 31/2005 | 143/18723 | 9.70e-05 | 1.18e-03 | 31 |
| GO:006032623 | Oral cavity | NEOLP | cell chemotaxis | 55/2005 | 310/18723 | 1.18e-04 | 1.40e-03 | 55 |
| GO:003162322 | Oral cavity | NEOLP | receptor internalization | 26/2005 | 113/18723 | 1.24e-04 | 1.47e-03 | 26 |
| GO:005114615 | Oral cavity | NEOLP | striated muscle cell differentiation | 51/2005 | 283/18723 | 1.37e-04 | 1.60e-03 | 51 |
| GO:004592621 | Oral cavity | NEOLP | negative regulation of growth | 46/2005 | 249/18723 | 1.58e-04 | 1.77e-03 | 46 |
| GO:005109031 | Oral cavity | NEOLP | regulation of DNA-binding transcription factor activity | 72/2005 | 440/18723 | 1.66e-04 | 1.84e-03 | 72 |
| GO:000165514 | Oral cavity | NEOLP | urogenital system development | 58/2005 | 338/18723 | 1.97e-04 | 2.13e-03 | 58 |
| GO:004825923 | Oral cavity | NEOLP | regulation of receptor-mediated endocytosis | 25/2005 | 110/18723 | 2.04e-04 | 2.19e-03 | 25 |
| GO:00614482 | Oral cavity | NEOLP | connective tissue development | 46/2005 | 252/18723 | 2.11e-04 | 2.25e-03 | 46 |
| GO:000268523 | Oral cavity | NEOLP | regulation of leukocyte migration | 40/2005 | 210/18723 | 2.14e-04 | 2.27e-03 | 40 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa043507 | Esophagus | ESCC | TGF-beta signaling pathway | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| hsa0435014 | Esophagus | ESCC | TGF-beta signaling pathway | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| hsa0435041 | Oral cavity | NEOLP | TGF-beta signaling pathway | 28/1112 | 108/8465 | 2.46e-04 | 1.62e-03 | 1.02e-03 | 28 |
| hsa0435051 | Oral cavity | NEOLP | TGF-beta signaling pathway | 28/1112 | 108/8465 | 2.46e-04 | 1.62e-03 | 1.02e-03 | 28 |
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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 |
| GREM1 | SNV | Missense_Mutation | c.332G>C | p.Arg111Pro | p.R111P | O60565 | protein_coding | deleterious(0) | probably_damaging(0.931) | TCGA-A2-A0YC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | PD | |
| GREM1 | insertion | Frame_Shift_Ins | novel | c.527_528insT | p.Arg177SerfsTer81 | p.R177Sfs*81 | O60565 | protein_coding | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| GREM1 | insertion | In_Frame_Ins | novel | c.529_530insATAAGCATTCACAGCTCAGGAAGCCTCAGGCTA | p.Arg177delinsHisLysHisSerGlnLeuArgLysProGlnAlaSer | p.R177delinsHKHSQLRKPQAS | O60565 | protein_coding | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| GREM1 | SNV | Missense_Mutation | novel | c.529N>T | p.Arg177Cys | p.R177C | O60565 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD |
| GREM1 | SNV | Missense_Mutation | c.461N>C | p.Val154Ala | p.V154A | O60565 | protein_coding | deleterious(0) | possibly_damaging(0.856) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GREM1 | SNV | Missense_Mutation | c.346N>A | p.Arg116Ser | p.R116S | O60565 | protein_coding | deleterious(0.03) | probably_damaging(0.991) | TCGA-AF-3911-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fu | PD | |
| GREM1 | SNV | Missense_Mutation | rs756849803 | c.347N>A | p.Arg116His | p.R116H | O60565 | protein_coding | deleterious(0.03) | probably_damaging(0.99) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| GREM1 | deletion | Frame_Shift_Del | c.99delN | p.Pro35ArgfsTer49 | p.P35Rfs*49 | O60565 | protein_coding | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |||
| GREM1 | SNV | Missense_Mutation | novel | c.135N>T | p.Glu45Asp | p.E45D | O60565 | protein_coding | tolerated(0.29) | benign(0.005) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| GREM1 | SNV | Missense_Mutation | novel | c.398N>C | p.Lys133Thr | p.K133T | O60565 | protein_coding | tolerated(0.08) | benign(0.076) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <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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