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Gene: CHI3L1 |
Gene summary for CHI3L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHI3L1 | Gene ID | 1116 |
| Gene name | chitinase 3 like 1 | |
| Gene Alias | ASRT7 | |
| Cytomap | 1q32.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A0A024R969 |
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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 |
| 1116 | CHI3L1 | GSM4909282 | Human | Breast | IDC | 3.58e-12 | 3.25e-01 | -0.0288 |
| 1116 | CHI3L1 | GSM4909285 | Human | Breast | IDC | 4.46e-04 | -2.30e-01 | 0.21 |
| 1116 | CHI3L1 | GSM4909286 | Human | Breast | IDC | 1.76e-12 | -4.27e-01 | 0.1081 |
| 1116 | CHI3L1 | GSM4909290 | Human | Breast | IDC | 3.77e-08 | -4.27e-01 | 0.2096 |
| 1116 | CHI3L1 | GSM4909291 | Human | Breast | IDC | 2.68e-08 | -4.33e-01 | 0.1753 |
| 1116 | CHI3L1 | GSM4909293 | Human | Breast | IDC | 6.19e-04 | -3.36e-01 | 0.1581 |
| 1116 | CHI3L1 | GSM4909294 | Human | Breast | IDC | 5.36e-13 | -4.02e-01 | 0.2022 |
| 1116 | CHI3L1 | GSM4909296 | Human | Breast | IDC | 5.75e-12 | -4.29e-01 | 0.1524 |
| 1116 | CHI3L1 | GSM4909297 | Human | Breast | IDC | 9.60e-13 | -4.12e-01 | 0.1517 |
| 1116 | CHI3L1 | GSM4909298 | Human | Breast | IDC | 1.81e-04 | -3.44e-01 | 0.1551 |
| 1116 | CHI3L1 | GSM4909299 | Human | Breast | IDC | 8.97e-06 | 5.51e-01 | 0.035 |
| 1116 | CHI3L1 | GSM4909301 | Human | Breast | IDC | 2.12e-16 | -4.33e-01 | 0.1577 |
| 1116 | CHI3L1 | GSM4909302 | Human | Breast | IDC | 1.05e-08 | -3.98e-01 | 0.1545 |
| 1116 | CHI3L1 | GSM4909304 | Human | Breast | IDC | 1.17e-02 | -3.11e-01 | 0.1636 |
| 1116 | CHI3L1 | GSM4909308 | Human | Breast | IDC | 2.56e-06 | -3.95e-01 | 0.158 |
| 1116 | CHI3L1 | GSM4909311 | Human | Breast | IDC | 3.34e-08 | -3.63e-01 | 0.1534 |
| 1116 | CHI3L1 | GSM4909312 | Human | Breast | IDC | 1.44e-09 | -4.16e-01 | 0.1552 |
| 1116 | CHI3L1 | GSM4909313 | Human | Breast | IDC | 2.89e-02 | 4.26e-01 | 0.0391 |
| 1116 | CHI3L1 | GSM4909315 | Human | Breast | IDC | 4.80e-16 | -4.31e-01 | 0.21 |
| 1116 | CHI3L1 | GSM4909316 | Human | Breast | IDC | 2.04e-03 | -4.33e-01 | 0.21 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00303249 | Esophagus | ESCC | lung development | 109/8552 | 177/18723 | 1.40e-05 | 1.27e-04 | 109 |
| GO:003461220 | Esophagus | ESCC | response to tumor necrosis factor | 149/8552 | 253/18723 | 1.47e-05 | 1.33e-04 | 149 |
| GO:007135620 | Esophagus | ESCC | cellular response to tumor necrosis factor | 132/8552 | 229/18723 | 1.69e-04 | 1.11e-03 | 132 |
| GO:000961216 | Esophagus | ESCC | response to mechanical stimulus | 124/8552 | 216/18723 | 3.30e-04 | 1.94e-03 | 124 |
| GO:19011362 | Esophagus | ESCC | carbohydrate derivative catabolic process | 99/8552 | 172/18723 | 1.11e-03 | 5.54e-03 | 99 |
| GO:000181916 | Esophagus | ESCC | positive regulation of cytokine production | 244/8552 | 467/18723 | 2.29e-03 | 1.01e-02 | 244 |
| GO:00380615 | Esophagus | ESCC | NIK/NF-kappaB signaling | 81/8552 | 143/18723 | 5.33e-03 | 2.00e-02 | 81 |
| GO:001810710 | Esophagus | ESCC | peptidyl-threonine phosphorylation | 66/8552 | 116/18723 | 9.76e-03 | 3.37e-02 | 66 |
| GO:00512161 | Esophagus | ESCC | cartilage development | 103/8552 | 190/18723 | 1.08e-02 | 3.67e-02 | 103 |
| GO:001821010 | Esophagus | ESCC | peptidyl-threonine modification | 70/8552 | 125/18723 | 1.29e-02 | 4.25e-02 | 70 |
| GO:1901136 | Liver | HCC | carbohydrate derivative catabolic process | 98/7958 | 172/18723 | 8.71e-05 | 7.62e-04 | 98 |
| GO:001810711 | Liver | HCC | peptidyl-threonine phosphorylation | 68/7958 | 116/18723 | 3.31e-04 | 2.33e-03 | 68 |
| GO:00705551 | Liver | HCC | response to interleukin-1 | 80/7958 | 143/18723 | 7.95e-04 | 4.77e-03 | 80 |
| GO:001821011 | Liver | HCC | peptidyl-threonine modification | 71/7958 | 125/18723 | 8.68e-04 | 5.14e-03 | 71 |
| GO:003461211 | Liver | HCC | response to tumor necrosis factor | 132/7958 | 253/18723 | 1.14e-03 | 6.48e-03 | 132 |
| GO:004586021 | Liver | HCC | positive regulation of protein kinase activity | 194/7958 | 386/18723 | 1.16e-03 | 6.54e-03 | 194 |
| GO:003367411 | Liver | HCC | positive regulation of kinase activity | 230/7958 | 467/18723 | 1.72e-03 | 8.95e-03 | 230 |
| GO:00096124 | Liver | HCC | response to mechanical stimulus | 113/7958 | 216/18723 | 2.20e-03 | 1.10e-02 | 113 |
| GO:00380611 | Liver | HCC | NIK/NF-kappaB signaling | 77/7958 | 143/18723 | 3.98e-03 | 1.76e-02 | 77 |
| GO:003032311 | Liver | HCC | respiratory tube development | 95/7958 | 181/18723 | 4.15e-03 | 1.81e-02 | 95 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
| CHI3L1 | SNV | Missense_Mutation | c.113N>T | p.Asp38Val | p.D38V | P36222 | protein_coding | tolerated(0.4) | benign(0.007) | TCGA-AN-A0XN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| CHI3L1 | SNV | Missense_Mutation | c.139G>A | p.Asp47Asn | p.D47N | P36222 | protein_coding | deleterious(0.03) | possibly_damaging(0.811) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| CHI3L1 | SNV | Missense_Mutation | c.217N>A | p.Asp73Asn | p.D73N | P36222 | protein_coding | deleterious(0.01) | probably_damaging(0.995) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| CHI3L1 | SNV | Missense_Mutation | rs376864309 | c.267C>A | p.Asn89Lys | p.N89K | P36222 | protein_coding | tolerated(0.95) | benign(0.007) | TCGA-BH-A8FZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CHI3L1 | SNV | Missense_Mutation | c.620N>G | p.Asp207Gly | p.D207G | P36222 | protein_coding | deleterious(0) | probably_damaging(0.96) | TCGA-C8-A135-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| CHI3L1 | SNV | Missense_Mutation | c.379N>G | p.Leu127Val | p.L127V | P36222 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E2-A15E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| CHI3L1 | SNV | Missense_Mutation | rs762736598 | c.185N>A | p.Ser62Asn | p.S62N | P36222 | protein_coding | tolerated(0.86) | benign(0.033) | TCGA-E9-A22E-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphane | SD |
| CHI3L1 | insertion | Nonsense_Mutation | novel | c.779_780insTAGGCACCTGGGATAGCCCTCTGGCTATGGGGCTGAGGTC | p.Phe261ArgfsTer5 | p.F261Rfs*5 | P36222 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| CHI3L1 | insertion | Nonsense_Mutation | novel | c.502_503insAGCTGCTATGAAAGTATTTTGGAAAGGGAAGT | p.Gly168GlufsTer4 | p.G168Efs*4 | P36222 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| CHI3L1 | insertion | Frame_Shift_Ins | novel | c.225_226insG | p.Leu76AlafsTer58 | p.L76Afs*58 | P36222 | protein_coding | TCGA-E2-A1LK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| 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 |
| 1116 | CHI3L1 | CELL SURFACE, DRUGGABLE GENOME | ANTI-INFLAMMATORY DRUGS | 16035398 | ||
| 1116 | CHI3L1 | CELL SURFACE, DRUGGABLE GENOME | CHEMOKINES | 15015934 |
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