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Gene: COL6A3 |
Gene summary for COL6A3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | COL6A3 | Gene ID | 1293 |
Gene name | collagen type VI alpha 3 chain | |
Gene Alias | BTHLM1 | |
Cytomap | 2q37.3 | |
Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | D9ZGF2 |
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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 |
1293 | COL6A3 | AEH-subject1 | Human | Endometrium | AEH | 3.00e-24 | -5.62e-01 | -0.3059 |
1293 | COL6A3 | AEH-subject2 | Human | Endometrium | AEH | 1.43e-27 | -5.88e-01 | -0.2525 |
1293 | COL6A3 | AEH-subject3 | Human | Endometrium | AEH | 2.14e-16 | -5.00e-01 | -0.2576 |
1293 | COL6A3 | AEH-subject4 | Human | Endometrium | AEH | 1.66e-03 | -2.89e-01 | -0.2657 |
1293 | COL6A3 | AEH-subject5 | Human | Endometrium | AEH | 5.26e-23 | -5.65e-01 | -0.2953 |
1293 | COL6A3 | EEC-subject1 | Human | Endometrium | EEC | 9.90e-26 | -5.86e-01 | -0.2682 |
1293 | COL6A3 | EEC-subject2 | Human | Endometrium | EEC | 1.26e-32 | -6.03e-01 | -0.2607 |
1293 | COL6A3 | EEC-subject3 | Human | Endometrium | EEC | 1.22e-25 | -5.23e-01 | -0.2525 |
1293 | COL6A3 | EEC-subject4 | Human | Endometrium | EEC | 9.17e-19 | -5.57e-01 | -0.2571 |
1293 | COL6A3 | EEC-subject5 | Human | Endometrium | EEC | 2.06e-26 | -5.83e-01 | -0.249 |
1293 | COL6A3 | GSM5276935 | Human | Endometrium | EEC | 2.25e-23 | -5.85e-01 | -0.123 |
1293 | COL6A3 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.68e-26 | -6.03e-01 | -0.1869 |
1293 | COL6A3 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 6.11e-21 | -5.84e-01 | -0.1875 |
1293 | COL6A3 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 2.23e-24 | -5.90e-01 | -0.1883 |
1293 | COL6A3 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 3.44e-28 | -5.61e-01 | -0.1934 |
1293 | COL6A3 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 8.01e-32 | -6.03e-01 | -0.1917 |
1293 | COL6A3 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 2.73e-35 | -6.03e-01 | -0.1916 |
1293 | COL6A3 | LZE2T | Human | Esophagus | ESCC | 6.17e-05 | 5.97e-01 | 0.082 |
1293 | COL6A3 | P4T-E | Human | Esophagus | ESCC | 2.18e-07 | 1.67e+00 | 0.1323 |
1293 | COL6A3 | P9T-E | Human | Esophagus | ESCC | 5.11e-06 | 1.52e+00 | 0.1131 |
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Transcriptomic changes along malignancy continuum. |
∗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:005254716 | Endometrium | AEH | regulation of peptidase activity | 85/2100 | 461/18723 | 2.47e-06 | 7.11e-05 | 85 |
GO:005254816 | Endometrium | AEH | regulation of endopeptidase activity | 76/2100 | 432/18723 | 4.42e-05 | 7.43e-04 | 76 |
GO:00075174 | Endometrium | AEH | muscle organ development | 60/2100 | 327/18723 | 8.19e-05 | 1.22e-03 | 60 |
GO:004586116 | Endometrium | AEH | negative regulation of proteolysis | 63/2100 | 351/18723 | 1.07e-04 | 1.53e-03 | 63 |
GO:005134610 | Endometrium | AEH | negative regulation of hydrolase activity | 65/2100 | 379/18723 | 3.18e-04 | 3.57e-03 | 65 |
GO:001046610 | Endometrium | AEH | negative regulation of peptidase activity | 43/2100 | 262/18723 | 6.78e-03 | 3.95e-02 | 43 |
GO:005254717 | Endometrium | EEC | regulation of peptidase activity | 91/2168 | 461/18723 | 2.00e-07 | 8.93e-06 | 91 |
GO:004586117 | Endometrium | EEC | negative regulation of proteolysis | 72/2168 | 351/18723 | 8.46e-07 | 2.98e-05 | 72 |
GO:005254817 | Endometrium | EEC | regulation of endopeptidase activity | 82/2168 | 432/18723 | 3.96e-06 | 1.04e-04 | 82 |
GO:005134615 | Endometrium | EEC | negative regulation of hydrolase activity | 72/2168 | 379/18723 | 1.46e-05 | 2.87e-04 | 72 |
GO:000751712 | Endometrium | EEC | muscle organ development | 59/2168 | 327/18723 | 3.49e-04 | 3.85e-03 | 59 |
GO:001046615 | Endometrium | EEC | negative regulation of peptidase activity | 49/2168 | 262/18723 | 4.64e-04 | 4.79e-03 | 49 |
GO:001095114 | Endometrium | EEC | negative regulation of endopeptidase activity | 47/2168 | 252/18723 | 6.37e-04 | 6.25e-03 | 47 |
GO:0052547111 | Esophagus | ESCC | regulation of peptidase activity | 275/8552 | 461/18723 | 7.54e-10 | 1.88e-08 | 275 |
GO:0052548111 | Esophagus | ESCC | regulation of endopeptidase activity | 253/8552 | 432/18723 | 3.68e-08 | 6.78e-07 | 253 |
GO:0045861111 | Esophagus | ESCC | negative regulation of proteolysis | 195/8552 | 351/18723 | 1.13e-04 | 7.85e-04 | 195 |
GO:0051346110 | Esophagus | ESCC | negative regulation of hydrolase activity | 208/8552 | 379/18723 | 1.76e-04 | 1.14e-03 | 208 |
GO:001046620 | Esophagus | ESCC | negative regulation of peptidase activity | 140/8552 | 262/18723 | 6.73e-03 | 2.46e-02 | 140 |
GO:001095119 | Esophagus | ESCC | negative regulation of endopeptidase activity | 135/8552 | 252/18723 | 6.86e-03 | 2.51e-02 | 135 |
GO:005254720 | Oral cavity | OSCC | regulation of peptidase activity | 255/7305 | 461/18723 | 5.78e-13 | 2.75e-11 | 255 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0451015 | Endometrium | AEH | Focal adhesion | 58/1197 | 203/8465 | 4.99e-08 | 7.37e-07 | 5.39e-07 | 58 |
hsa0451016 | Endometrium | AEH | Focal adhesion | 58/1197 | 203/8465 | 4.99e-08 | 7.37e-07 | 5.39e-07 | 58 |
hsa0451024 | Endometrium | EEC | Focal adhesion | 58/1237 | 203/8465 | 1.61e-07 | 2.30e-06 | 1.71e-06 | 58 |
hsa0451034 | Endometrium | EEC | Focal adhesion | 58/1237 | 203/8465 | 1.61e-07 | 2.30e-06 | 1.71e-06 | 58 |
hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0451020 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa04510111 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
hsa0415114 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
hsa051659 | Oral cavity | OSCC | Human papillomavirus infection | 200/3704 | 331/8465 | 3.83e-10 | 4.93e-09 | 2.51e-09 | 200 |
hsa0451019 | Oral cavity | OSCC | Focal adhesion | 128/3704 | 203/8465 | 1.71e-08 | 1.63e-07 | 8.31e-08 | 128 |
hsa041516 | Oral cavity | OSCC | PI3K-Akt signaling pathway | 185/3704 | 354/8465 | 6.26e-04 | 1.86e-03 | 9.49e-04 | 185 |
hsa0516514 | Oral cavity | OSCC | Human papillomavirus infection | 200/3704 | 331/8465 | 3.83e-10 | 4.93e-09 | 2.51e-09 | 200 |
hsa04510110 | Oral cavity | OSCC | Focal adhesion | 128/3704 | 203/8465 | 1.71e-08 | 1.63e-07 | 8.31e-08 | 128 |
hsa0415113 | Oral cavity | OSCC | PI3K-Akt signaling pathway | 185/3704 | 354/8465 | 6.26e-04 | 1.86e-03 | 9.49e-04 | 185 |
hsa0451043 | Oral cavity | NEOLP | Focal adhesion | 71/1112 | 203/8465 | 7.25e-16 | 7.68e-14 | 4.83e-14 | 71 |
hsa0516561 | Oral cavity | NEOLP | Human papillomavirus infection | 90/1112 | 331/8465 | 2.75e-12 | 1.75e-10 | 1.10e-10 | 90 |
hsa0415141 | Oral cavity | NEOLP | PI3K-Akt signaling pathway | 79/1112 | 354/8465 | 8.42e-07 | 9.92e-06 | 6.24e-06 | 79 |
hsa045126 | Oral cavity | NEOLP | ECM-receptor interaction | 24/1112 | 89/8465 | 3.56e-04 | 2.18e-03 | 1.37e-03 | 24 |
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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 |
COL6A3 | ITGA1_ITGB1 | COL6A3_ITGA1_ITGB1 | COLLAGEN | Breast | ADJ |
COL6A3 | ITGA2_ITGB1 | COL6A3_ITGA2_ITGB1 | COLLAGEN | Breast | ADJ |
COL6A3 | CD44 | COL6A3_CD44 | COLLAGEN | Breast | ADJ |
COL6A3 | SDC4 | COL6A3_SDC4 | COLLAGEN | Breast | ADJ |
COL6A3 | ITGA1_ITGB1 | COL6A3_ITGA1_ITGB1 | COLLAGEN | Breast | DCIS |
COL6A3 | ITGA2_ITGB1 | COL6A3_ITGA2_ITGB1 | COLLAGEN | Breast | DCIS |
COL6A3 | CD44 | COL6A3_CD44 | COLLAGEN | Breast | DCIS |
COL6A3 | SDC1 | COL6A3_SDC1 | COLLAGEN | Breast | DCIS |
COL6A3 | SDC4 | COL6A3_SDC4 | COLLAGEN | Breast | DCIS |
COL6A3 | ITGA1_ITGB1 | COL6A3_ITGA1_ITGB1 | COLLAGEN | Breast | Healthy |
COL6A3 | ITGA2_ITGB1 | COL6A3_ITGA2_ITGB1 | COLLAGEN | Breast | Healthy |
COL6A3 | ITGAV_ITGB8 | COL6A3_ITGAV_ITGB8 | COLLAGEN | Breast | Healthy |
COL6A3 | CD44 | COL6A3_CD44 | COLLAGEN | Breast | Healthy |
COL6A3 | SDC1 | COL6A3_SDC1 | COLLAGEN | Breast | Healthy |
COL6A3 | SDC4 | COL6A3_SDC4 | COLLAGEN | Breast | Healthy |
COL6A3 | ITGA1_ITGB1 | COL6A3_ITGA1_ITGB1 | COLLAGEN | Breast | IDC |
COL6A3 | CD44 | COL6A3_CD44 | COLLAGEN | Breast | IDC |
COL6A3 | SDC1 | COL6A3_SDC1 | COLLAGEN | Breast | IDC |
COL6A3 | SDC4 | COL6A3_SDC4 | COLLAGEN | Breast | IDC |
COL6A3 | ITGA1_ITGB1 | COL6A3_ITGA1_ITGB1 | COLLAGEN | Breast | Precancer |
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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 |
COL6A3 | SNV | Missense_Mutation | novel | c.6661N>C | p.Glu2221Gln | p.E2221Q | P12111 | protein_coding | tolerated(0.42) | benign(0) | TCGA-55-6982-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | gemzar | PD |
COL6A3 | SNV | Missense_Mutation | novel | c.3156N>C | p.Gln1052His | p.Q1052H | P12111 | protein_coding | deleterious(0.01) | possibly_damaging(0.776) | TCGA-55-6982-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | gemzar | PD |
COL6A3 | SNV | Missense_Mutation | novel | c.8722N>A | p.Ala2908Thr | p.A2908T | P12111 | protein_coding | tolerated(0.26) | benign(0.052) | TCGA-55-7576-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | alimta | CR |
COL6A3 | SNV | Missense_Mutation | c.9116N>A | p.Thr3039Lys | p.T3039K | P12111 | protein_coding | deleterious(0) | benign(0.279) | TCGA-55-7994-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | CR | |
COL6A3 | SNV | Missense_Mutation | c.3709N>T | p.Leu1237Phe | p.L1237F | P12111 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-55-7995-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | CR | |
COL6A3 | SNV | Missense_Mutation | c.5653N>C | p.Val1885Leu | p.V1885L | P12111 | protein_coding | deleterious(0) | possibly_damaging(0.845) | TCGA-55-8205-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | |
COL6A3 | SNV | Missense_Mutation | c.5901N>T | p.Glu1967Asp | p.E1967D | P12111 | protein_coding | tolerated(0.07) | benign(0.34) | TCGA-55-8299-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
COL6A3 | SNV | Missense_Mutation | c.4120N>A | p.Asp1374Asn | p.D1374N | P12111 | protein_coding | tolerated(0.06) | possibly_damaging(0.875) | TCGA-55-8507-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
COL6A3 | SNV | Missense_Mutation | rs200825417 | c.4690N>T | p.Arg1564Cys | p.R1564C | P12111 | protein_coding | deleterious(0.01) | possibly_damaging(0.448) | TCGA-55-A490-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD |
COL6A3 | SNV | Missense_Mutation | c.3861C>G | p.Asn1287Lys | p.N1287K | P12111 | protein_coding | deleterious(0.03) | possibly_damaging(0.751) | TCGA-64-5775-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | carboplatin | PD |
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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 |
1293 | COL6A3 | DRUGGABLE GENOME, PROTEASE INHIBITOR | CHEMBL2108709 | COLLAGENASE CLOSTRIDIUM HISTOLYTICUM | ||
1293 | COL6A3 | DRUGGABLE GENOME, PROTEASE INHIBITOR | CHEMBL2095222 | OCRIPLASMIN |
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