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Gene: CHST3 |
Gene summary for CHST3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHST3 | Gene ID | 9469 |
| Gene name | carbohydrate sulfotransferase 3 | |
| Gene Alias | C6ST | |
| Cytomap | 10q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | Q7LGC8 |
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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 |
| 9469 | CHST3 | P2T-E | Human | Esophagus | ESCC | 1.25e-17 | 2.98e-01 | 0.1177 |
| 9469 | CHST3 | P5T-E | Human | Esophagus | ESCC | 3.35e-19 | 1.10e-01 | 0.1327 |
| 9469 | CHST3 | P8T-E | Human | Esophagus | ESCC | 3.82e-03 | -7.51e-02 | 0.0889 |
| 9469 | CHST3 | P10T-E | Human | Esophagus | ESCC | 1.37e-04 | 4.01e-02 | 0.116 |
| 9469 | CHST3 | P11T-E | Human | Esophagus | ESCC | 3.35e-11 | 6.88e-01 | 0.1426 |
| 9469 | CHST3 | P12T-E | Human | Esophagus | ESCC | 2.68e-09 | 1.58e-01 | 0.1122 |
| 9469 | CHST3 | P15T-E | Human | Esophagus | ESCC | 3.14e-15 | 1.37e-01 | 0.1149 |
| 9469 | CHST3 | P16T-E | Human | Esophagus | ESCC | 1.78e-21 | 3.99e-01 | 0.1153 |
| 9469 | CHST3 | P20T-E | Human | Esophagus | ESCC | 2.51e-07 | 7.21e-02 | 0.1124 |
| 9469 | CHST3 | P21T-E | Human | Esophagus | ESCC | 9.76e-16 | 2.59e-01 | 0.1617 |
| 9469 | CHST3 | P22T-E | Human | Esophagus | ESCC | 8.85e-19 | 8.23e-02 | 0.1236 |
| 9469 | CHST3 | P24T-E | Human | Esophagus | ESCC | 5.19e-10 | 3.53e-01 | 0.1287 |
| 9469 | CHST3 | P26T-E | Human | Esophagus | ESCC | 1.31e-12 | 6.15e-02 | 0.1276 |
| 9469 | CHST3 | P27T-E | Human | Esophagus | ESCC | 3.58e-14 | 1.98e-01 | 0.1055 |
| 9469 | CHST3 | P28T-E | Human | Esophagus | ESCC | 1.79e-16 | 9.81e-02 | 0.1149 |
| 9469 | CHST3 | P30T-E | Human | Esophagus | ESCC | 5.95e-16 | 5.21e-01 | 0.137 |
| 9469 | CHST3 | P31T-E | Human | Esophagus | ESCC | 5.31e-08 | -2.00e-02 | 0.1251 |
| 9469 | CHST3 | P32T-E | Human | Esophagus | ESCC | 1.03e-04 | 2.56e-01 | 0.1666 |
| 9469 | CHST3 | P36T-E | Human | Esophagus | ESCC | 8.84e-12 | 3.41e-01 | 0.1187 |
| 9469 | CHST3 | P37T-E | Human | Esophagus | ESCC | 1.92e-02 | 1.38e-01 | 0.1371 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:00091002 | Esophagus | ESCC | glycoprotein metabolic process | 226/8552 | 387/18723 | 2.64e-07 | 3.94e-06 | 226 |
| GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:00442725 | Esophagus | ESCC | sulfur compound biosynthetic process | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
| GO:00091012 | Esophagus | ESCC | glycoprotein biosynthetic process | 181/8552 | 317/18723 | 2.54e-05 | 2.15e-04 | 181 |
| GO:0006029 | Esophagus | ESCC | proteoglycan metabolic process | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
| GO:0030166 | Esophagus | ESCC | proteoglycan biosynthetic process | 35/8552 | 56/18723 | 8.30e-03 | 2.94e-02 | 35 |
| GO:0006024 | Esophagus | ESCC | glycosaminoglycan biosynthetic process | 45/8552 | 75/18723 | 8.75e-03 | 3.08e-02 | 45 |
| GO:0006023 | Esophagus | ESCC | aminoglycan biosynthetic process | 47/8552 | 79/18723 | 9.29e-03 | 3.23e-02 | 47 |
| GO:00442724 | Oral cavity | OSCC | sulfur compound biosynthetic process | 82/7305 | 148/18723 | 3.71e-05 | 3.31e-04 | 82 |
| GO:00067905 | Oral cavity | OSCC | sulfur compound metabolic process | 168/7305 | 339/18723 | 4.50e-05 | 3.84e-04 | 168 |
| GO:0030206 | Oral cavity | OSCC | chondroitin sulfate biosynthetic process | 15/7305 | 18/18723 | 1.53e-04 | 1.07e-03 | 15 |
| GO:00091001 | Oral cavity | OSCC | glycoprotein metabolic process | 185/7305 | 387/18723 | 2.37e-04 | 1.54e-03 | 185 |
| GO:00091011 | Oral cavity | OSCC | glycoprotein biosynthetic process | 151/7305 | 317/18723 | 1.01e-03 | 5.26e-03 | 151 |
| GO:0050650 | Oral cavity | OSCC | chondroitin sulfate proteoglycan biosynthetic process | 16/7305 | 23/18723 | 2.93e-03 | 1.27e-02 | 16 |
| GO:0030204 | Oral cavity | OSCC | chondroitin sulfate metabolic process | 19/7305 | 30/18723 | 6.03e-03 | 2.28e-02 | 19 |
| GO:0006040 | Oral cavity | OSCC | amino sugar metabolic process | 24/7305 | 42/18723 | 1.30e-02 | 4.34e-02 | 24 |
| GO:000679012 | Oral cavity | LP | sulfur compound metabolic process | 106/4623 | 339/18723 | 3.36e-03 | 2.25e-02 | 106 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00532 | Oral cavity | OSCC | Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | 16/3704 | 21/8465 | 2.61e-03 | 6.77e-03 | 3.45e-03 | 16 |
| hsa005321 | Oral cavity | OSCC | Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate | 16/3704 | 21/8465 | 2.61e-03 | 6.77e-03 | 3.45e-03 | 16 |
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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 |
| CHST3 | SNV | Missense_Mutation | novel | c.1391N>G | p.Asn464Ser | p.N464S | Q7LGC8 | protein_coding | deleterious(0) | possibly_damaging(0.696) | TCGA-S3-AA11-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | letrozole | CR |
| CHST3 | insertion | In_Frame_Ins | novel | c.391_392insTTAACATTTCTGAGTCTT | p.Pro131delinsLeuAsnIleSerGluSerSer | p.P131delinsLNISESS | Q7LGC8 | protein_coding | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD | ||
| CHST3 | insertion | Nonsense_Mutation | novel | c.133_134insGGTAGAATTTATGCGCTATGATATTTTTTTCTTTCGTTAATTTTT | p.Ile45delinsArgTerAsnLeuCysAlaMetIlePhePheSerPheValAsnPheLeu | p.I45delinsR*NLCAMIFFSFVNFL | Q7LGC8 | protein_coding | TCGA-BH-A0EB-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| CHST3 | SNV | Missense_Mutation | c.229C>T | p.Leu77Phe | p.L77F | Q7LGC8 | protein_coding | tolerated(0.2) | benign(0.045) | TCGA-C5-A1BL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CHST3 | SNV | Missense_Mutation | c.545N>T | p.Ala182Val | p.A182V | Q7LGC8 | protein_coding | tolerated(0.44) | benign(0.017) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| CHST3 | SNV | Missense_Mutation | rs768518290 | c.553N>A | p.Ala185Thr | p.A185T | Q7LGC8 | protein_coding | tolerated(0.09) | possibly_damaging(0.757) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
| CHST3 | SNV | Missense_Mutation | rs767508669 | c.398N>A | p.Arg133His | p.R133H | Q7LGC8 | protein_coding | deleterious(0.01) | possibly_damaging(0.595) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| CHST3 | SNV | Missense_Mutation | c.986N>C | p.Gly329Ala | p.G329A | Q7LGC8 | protein_coding | deleterious(0.05) | probably_damaging(0.972) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| CHST3 | SNV | Missense_Mutation | rs866792272 | c.1378G>A | p.Ala460Thr | p.A460T | Q7LGC8 | protein_coding | tolerated(0.2) | benign(0.009) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD |
| CHST3 | SNV | Missense_Mutation | c.902G>A | p.Arg301His | p.R301H | Q7LGC8 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D5-6930-01 | 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 |
| 9469 | CHST3 | DRUGGABLE GENOME, ENZYME | thalidomide | THALIDOMIDE | 20038957 | |
| 9469 | CHST3 | DRUGGABLE GENOME, ENZYME | docetaxel | DOCETAXEL | 20038957 |
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