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Gene: CHRD |
Gene summary for CHRD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHRD | Gene ID | 8646 |
| Gene name | chordin | |
| Gene Alias | CHRD | |
| Cytomap | 3q27.1 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | E7ESX1 |
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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 |
| 8646 | CHRD | HCC1_Meng | Human | Liver | HCC | 3.88e-26 | 6.41e-02 | 0.0246 |
| 8646 | CHRD | HCC2 | Human | Liver | HCC | 3.81e-11 | 2.32e+00 | 0.5341 |
| 8646 | CHRD | S014 | Human | Liver | HCC | 2.07e-17 | 9.07e-01 | 0.2254 |
| 8646 | CHRD | S015 | Human | Liver | HCC | 1.29e-26 | 1.36e+00 | 0.2375 |
| 8646 | CHRD | S016 | Human | Liver | HCC | 4.30e-34 | 1.19e+00 | 0.2243 |
| 8646 | CHRD | S028 | Human | Liver | HCC | 1.19e-05 | 3.60e-01 | 0.2503 |
| 8646 | CHRD | S029 | Human | Liver | HCC | 6.50e-03 | 3.52e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:004578512 | Liver | HCC | positive regulation of cell adhesion | 215/7958 | 437/18723 | 2.53e-03 | 1.22e-02 | 215 |
| GO:00219154 | Liver | HCC | neural tube development | 82/7958 | 152/18723 | 2.83e-03 | 1.33e-02 | 82 |
| GO:000164911 | Liver | HCC | osteoblast differentiation | 115/7958 | 229/18723 | 1.08e-02 | 3.99e-02 | 115 |
| GO:000150310 | Oral cavity | OSCC | ossification | 203/7305 | 408/18723 | 5.54e-06 | 6.19e-05 | 203 |
| GO:000150315 | Oral cavity | LP | ossification | 123/4623 | 408/18723 | 6.55e-03 | 3.84e-02 | 123 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| CHRD | SNV | Missense_Mutation | c.516C>G | p.Phe172Leu | p.F172L | Q9H2X0 | protein_coding | deleterious(0) | possibly_damaging(0.747) | TCGA-A8-A07P-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
| CHRD | SNV | Missense_Mutation | rs760703245 | c.1789N>T | p.Arg597Trp | p.R597W | Q9H2X0 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A8-A07Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unspecific | Exemestane | SD |
| CHRD | SNV | Missense_Mutation | c.2641N>C | p.Glu881Gln | p.E881Q | Q9H2X0 | protein_coding | tolerated(0.05) | possibly_damaging(0.632) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CHRD | SNV | Missense_Mutation | c.1108N>A | p.Glu370Lys | p.E370K | Q9H2X0 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-B6-A0WZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| CHRD | SNV | Missense_Mutation | c.2201N>A | p.Arg734Gln | p.R734Q | Q9H2X0 | protein_coding | deleterious(0.02) | possibly_damaging(0.849) | TCGA-BH-A18K-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| CHRD | SNV | Missense_Mutation | rs771198668 | c.1925G>A | p.Arg642Gln | p.R642Q | Q9H2X0 | protein_coding | tolerated(0.06) | benign(0.319) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CHRD | SNV | Missense_Mutation | c.1678G>A | p.Asp560Asn | p.D560N | Q9H2X0 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| CHRD | SNV | Missense_Mutation | c.2847G>C | p.Glu949Asp | p.E949D | Q9H2X0 | protein_coding | tolerated_low_confidence(0.13) | benign(0.046) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| CHRD | SNV | Missense_Mutation | novel | c.1790N>T | p.Arg597Leu | p.R597L | Q9H2X0 | protein_coding | tolerated(0.1) | probably_damaging(0.909) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| CHRD | SNV | Missense_Mutation | c.1527N>A | p.Asp509Glu | p.D509E | Q9H2X0 | protein_coding | tolerated(0.43) | benign(0.216) | TCGA-A6-5659-01 | 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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