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Gene: COLGALT2 |
Gene summary for COLGALT2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | COLGALT2 | Gene ID | 23127 |
Gene name | collagen beta(1-O)galactosyltransferase 2 | |
Gene Alias | C1orf17 | |
Cytomap | 1q25.3 | |
Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | B4DF84 |
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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 |
23127 | COLGALT2 | male-WTA | Human | Thyroid | PTC | 1.89e-03 | 7.66e-02 | 0.1037 |
23127 | COLGALT2 | PTC04 | Human | Thyroid | PTC | 4.82e-02 | 1.10e-01 | 0.1927 |
23127 | COLGALT2 | ATC13 | Human | Thyroid | ATC | 1.18e-45 | 9.32e-01 | 0.34 |
23127 | COLGALT2 | ATC5 | Human | Thyroid | ATC | 5.76e-46 | 9.77e-01 | 0.34 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00301986 | Thyroid | PTC | extracellular matrix organization | 124/5968 | 301/18723 | 3.75e-04 | 2.53e-03 | 124 |
GO:00430626 | Thyroid | PTC | extracellular structure organization | 124/5968 | 302/18723 | 4.38e-04 | 2.92e-03 | 124 |
GO:00452296 | Thyroid | PTC | external encapsulating structure organization | 124/5968 | 304/18723 | 5.96e-04 | 3.79e-03 | 124 |
GO:00301995 | Thyroid | PTC | collagen fibril organization | 29/5968 | 61/18723 | 7.57e-03 | 3.23e-02 | 29 |
GO:003019812 | Thyroid | ATC | extracellular matrix organization | 152/6293 | 301/18723 | 8.63e-10 | 2.24e-08 | 152 |
GO:004306212 | Thyroid | ATC | extracellular structure organization | 152/6293 | 302/18723 | 1.17e-09 | 2.94e-08 | 152 |
GO:004522912 | Thyroid | ATC | external encapsulating structure organization | 152/6293 | 304/18723 | 2.11e-09 | 5.08e-08 | 152 |
GO:003019911 | Thyroid | ATC | collagen fibril organization | 43/6293 | 61/18723 | 4.24e-09 | 9.57e-08 | 43 |
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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 |
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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 |
COLGALT2 | SNV | Missense_Mutation | rs368641256 | c.458G>A | p.Arg153Gln | p.R153Q | Q8IYK4 | protein_coding | tolerated(0.34) | benign(0.087) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
COLGALT2 | SNV | Missense_Mutation | c.410N>A | p.Pro137Gln | p.P137Q | Q8IYK4 | protein_coding | deleterious(0.04) | possibly_damaging(0.709) | TCGA-AO-A0JD-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | |
COLGALT2 | SNV | Missense_Mutation | novel | c.608G>T | p.Trp203Leu | p.W203L | Q8IYK4 | protein_coding | deleterious(0) | possibly_damaging(0.816) | TCGA-E2-A15M-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
COLGALT2 | deletion | Frame_Shift_Del | novel | c.1034delT | p.Phe345SerfsTer2 | p.F345Sfs*2 | Q8IYK4 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
COLGALT2 | SNV | Missense_Mutation | novel | c.964N>T | p.Pro322Ser | p.P322S | Q8IYK4 | protein_coding | deleterious(0.01) | benign(0.41) | TCGA-C5-A7X5-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
COLGALT2 | SNV | Missense_Mutation | c.1205N>T | p.Ser402Phe | p.S402F | Q8IYK4 | protein_coding | deleterious(0.02) | probably_damaging(0.917) | TCGA-EK-A2H0-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
COLGALT2 | SNV | Missense_Mutation | c.1205N>T | p.Ser402Phe | p.S402F | Q8IYK4 | protein_coding | deleterious(0.02) | probably_damaging(0.917) | TCGA-ZJ-A8QQ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
COLGALT2 | SNV | Missense_Mutation | rs779082349 | c.767N>T | p.Pro256Leu | p.P256L | Q8IYK4 | protein_coding | deleterious(0.04) | possibly_damaging(0.902) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
COLGALT2 | SNV | Missense_Mutation | c.8N>T | p.Ala3Val | p.A3V | Q8IYK4 | protein_coding | deleterious_low_confidence(0.01) | benign(0) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
COLGALT2 | SNV | Missense_Mutation | rs753492954 | c.1679N>T | p.Thr560Met | p.T560M | Q8IYK4 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | 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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