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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:00713473 | Oral cavity | OSCC | cellular response to interleukin-1 | 58/7305 | 113/18723 | 5.14e-03 | 2.01e-02 | 58 |
| GO:00518976 | Oral cavity | OSCC | positive regulation of protein kinase B signaling | 61/7305 | 120/18723 | 5.52e-03 | 2.14e-02 | 61 |
| GO:00434107 | Oral cavity | OSCC | positive regulation of MAPK cascade | 213/7305 | 480/18723 | 8.71e-03 | 3.16e-02 | 213 |
| GO:00703716 | Oral cavity | OSCC | ERK1 and ERK2 cascade | 150/7305 | 330/18723 | 9.47e-03 | 3.38e-02 | 150 |
| GO:00518967 | Oral cavity | OSCC | regulation of protein kinase B signaling | 88/7305 | 185/18723 | 1.07e-02 | 3.64e-02 | 88 |
| GO:0006040 | Oral cavity | OSCC | amino sugar metabolic process | 24/7305 | 42/18723 | 1.30e-02 | 4.34e-02 | 24 |
| GO:00703724 | Oral cavity | OSCC | regulation of ERK1 and ERK2 cascade | 140/7305 | 309/18723 | 1.34e-02 | 4.46e-02 | 140 |
| GO:0046348 | Oral cavity | OSCC | amino sugar catabolic process | 10/7305 | 14/18723 | 1.44e-02 | 4.69e-02 | 10 |
| GO:000961217 | Skin | AK | response to mechanical stimulus | 42/1910 | 216/18723 | 3.07e-05 | 5.21e-04 | 42 |
| GO:003367424 | Skin | AK | positive regulation of kinase activity | 73/1910 | 467/18723 | 1.42e-04 | 1.71e-03 | 73 |
| GO:007135624 | Skin | AK | cellular response to tumor necrosis factor | 40/1910 | 229/18723 | 4.98e-04 | 4.58e-03 | 40 |
| GO:00518977 | Skin | AK | positive regulation of protein kinase B signaling | 24/1910 | 120/18723 | 9.53e-04 | 7.64e-03 | 24 |
| GO:003032410 | Skin | AK | lung development | 32/1910 | 177/18723 | 9.60e-04 | 7.68e-03 | 32 |
| GO:003032310 | Skin | AK | respiratory tube development | 32/1910 | 181/18723 | 1.41e-03 | 1.04e-02 | 32 |
| GO:00434917 | Skin | AK | protein kinase B signaling | 36/1910 | 211/18723 | 1.42e-03 | 1.05e-02 | 36 |
| GO:004586019 | Skin | AK | positive regulation of protein kinase activity | 58/1910 | 386/18723 | 1.71e-03 | 1.20e-02 | 58 |
| GO:003461225 | Skin | AK | response to tumor necrosis factor | 41/1910 | 253/18723 | 1.92e-03 | 1.31e-02 | 41 |
| GO:00705557 | Skin | AK | response to interleukin-1 | 26/1910 | 143/18723 | 2.53e-03 | 1.63e-02 | 26 |
| GO:000181917 | Skin | AK | positive regulation of cytokine production | 67/1910 | 467/18723 | 2.59e-03 | 1.67e-02 | 67 |
| GO:00605418 | Skin | AK | respiratory system development | 34/1910 | 203/18723 | 2.60e-03 | 1.67e-02 | 34 |
| 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 |
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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. |
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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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