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Gene: CSGALNACT1 |
Gene summary for CSGALNACT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CSGALNACT1 | Gene ID | 55790 |
| Gene name | chondroitin sulfate N-acetylgalactosaminyltransferase 1 | |
| Gene Alias | CSGalNAcT-1 | |
| Cytomap | 8p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0000271 | UniProtAcc | Q8TDX6 |
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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 |
| 55790 | CSGALNACT1 | C08 | Human | Oral cavity | OSCC | 1.81e-02 | 1.16e-02 | 0.1919 |
| 55790 | CSGALNACT1 | EOLP-1 | Human | Oral cavity | EOLP | 9.81e-15 | 5.56e-01 | -0.0202 |
| 55790 | CSGALNACT1 | NEOLP-1 | Human | Oral cavity | NEOLP | 1.06e-21 | 8.25e-01 | -0.0194 |
| 55790 | CSGALNACT1 | 047563_1562-all-cells | Human | Prostate | BPH | 1.91e-10 | 4.93e-01 | 0.0791 |
| 55790 | CSGALNACT1 | 048752_1579-all-cells | Human | Prostate | BPH | 1.34e-27 | 6.72e-01 | 0.1008 |
| 55790 | CSGALNACT1 | 052095_1628-all-cells | Human | Prostate | BPH | 5.18e-21 | 5.96e-01 | 0.1032 |
| 55790 | CSGALNACT1 | 052097_1595-all-cells | Human | Prostate | BPH | 6.82e-06 | 2.86e-01 | 0.0972 |
| 55790 | CSGALNACT1 | 052099_1652-all-cells | Human | Prostate | BPH | 2.51e-13 | 4.32e-01 | 0.1038 |
| 55790 | CSGALNACT1 | Dong_P1 | Human | Prostate | Tumor | 5.89e-05 | 5.16e-02 | 0.035 |
| 55790 | CSGALNACT1 | Dong_P5 | Human | Prostate | Tumor | 1.89e-12 | 2.75e-02 | 0.053 |
| 55790 | CSGALNACT1 | GSM5353240_PA_PR5254_T1_S15_L001 | Human | Prostate | Tumor | 2.42e-02 | 3.13e-01 | 0.1575 |
| 55790 | CSGALNACT1 | Adj_PTCwithHT_6 | Human | Thyroid | HT | 8.96e-03 | -2.71e-01 | 0.02 |
| 55790 | CSGALNACT1 | PTCwithHT_6 | Human | Thyroid | HT | 1.15e-03 | -2.59e-01 | 0.02 |
| 55790 | CSGALNACT1 | PTCwithHT_8 | Human | Thyroid | HT | 2.01e-02 | -2.54e-01 | 0.0351 |
| 55790 | CSGALNACT1 | PTCwithoutHT_2 | Human | Thyroid | PTC | 1.28e-03 | -2.64e-01 | 0.0419 |
| 55790 | CSGALNACT1 | male-WTA | Human | Thyroid | PTC | 1.22e-19 | -2.52e-02 | 0.1037 |
| 55790 | CSGALNACT1 | PTC01 | Human | Thyroid | PTC | 4.17e-11 | -1.93e-01 | 0.1899 |
| 55790 | CSGALNACT1 | PTC06 | Human | Thyroid | PTC | 5.20e-09 | 6.12e-02 | 0.2057 |
| 55790 | CSGALNACT1 | PTC07 | Human | Thyroid | PTC | 5.10e-22 | 1.74e-01 | 0.2044 |
| 55790 | CSGALNACT1 | ATC12 | Human | Thyroid | ATC | 2.95e-05 | -1.22e-01 | 0.34 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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: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:00092255 | Oral cavity | OSCC | nucleotide-sugar metabolic process | 26/7305 | 36/18723 | 5.44e-05 | 4.51e-04 | 26 |
| 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:00160513 | Oral cavity | OSCC | carbohydrate biosynthetic process | 97/7305 | 202/18723 | 5.50e-03 | 2.13e-02 | 97 |
| GO:0030204 | Oral cavity | OSCC | chondroitin sulfate metabolic process | 19/7305 | 30/18723 | 6.03e-03 | 2.28e-02 | 19 |
| GO:00442625 | Oral cavity | OSCC | cellular carbohydrate metabolic process | 130/7305 | 283/18723 | 9.98e-03 | 3.49e-02 | 130 |
| GO:0006040 | Oral cavity | OSCC | amino sugar metabolic process | 24/7305 | 42/18723 | 1.30e-02 | 4.34e-02 | 24 |
| GO:00442624 | Prostate | BPH | cellular carbohydrate metabolic process | 66/3107 | 283/18723 | 2.06e-03 | 1.16e-02 | 66 |
| GO:00442723 | Prostate | BPH | sulfur compound biosynthetic process | 37/3107 | 148/18723 | 5.70e-03 | 2.65e-02 | 37 |
| GO:004426212 | Prostate | Tumor | cellular carbohydrate metabolic process | 66/3246 | 283/18723 | 5.90e-03 | 2.74e-02 | 66 |
| GO:004427211 | Prostate | Tumor | sulfur compound biosynthetic process | 38/3246 | 148/18723 | 6.69e-03 | 3.06e-02 | 38 |
| GO:00092257 | Thyroid | PTC | nucleotide-sugar metabolic process | 23/5968 | 36/18723 | 7.78e-05 | 6.66e-04 | 23 |
| GO:00442726 | Thyroid | PTC | sulfur compound biosynthetic process | 63/5968 | 148/18723 | 3.91e-03 | 1.87e-02 | 63 |
| GO:00091013 | Thyroid | PTC | glycoprotein biosynthetic process | 123/5968 | 317/18723 | 5.05e-03 | 2.33e-02 | 123 |
| GO:00091003 | Thyroid | PTC | glycoprotein metabolic process | 147/5968 | 387/18723 | 5.87e-03 | 2.64e-02 | 147 |
| GO:000922511 | Thyroid | ATC | nucleotide-sugar metabolic process | 24/6293 | 36/18723 | 5.10e-05 | 3.99e-04 | 24 |
| Page: 1 2 |
| 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 |
| 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 |
| CSGALNACT1 | SNV | Missense_Mutation | rs199989662 | c.1397N>A | p.Arg466Gln | p.R466Q | Q8TDX6 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-B6-A0RH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| CSGALNACT1 | insertion | In_Frame_Ins | novel | c.152_153insACTGGGTCTTAGGGTATTTTCCTGTCCCCACTCCGCCTT | p.Pro51_Thr52insLeuGlyLeuArgValPheSerCysProHisSerAlaPhe | p.P51_T52insLGLRVFSCPHSAF | Q8TDX6 | protein_coding | TCGA-A8-A07Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unspecific | Exemestane | SD | ||
| CSGALNACT1 | insertion | Nonsense_Mutation | novel | c.269_270insGGAAAATCATTAAACATCATTAAAAAAAAAAATCCT | p.Ser90delinsArgGluAsnHisTerThrSerLeuLysLysLysIleLeu | p.S90delinsRENH*TSLKKKIL | Q8TDX6 | protein_coding | TCGA-AN-A0FV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| CSGALNACT1 | insertion | Nonsense_Mutation | novel | c.1511_1512insAAAGGAAACTCATTCAGACTGGTGATATCGT | p.His504GlnfsTer9 | p.H504Qfs*9 | Q8TDX6 | protein_coding | TCGA-BH-A0B4-01 | Breast | breast invasive carcinoma | Male | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | ||
| CSGALNACT1 | deletion | Frame_Shift_Del | novel | c.37delN | p.Ser13ProfsTer60 | p.S13Pfs*60 | Q8TDX6 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CSGALNACT1 | deletion | Frame_Shift_Del | novel | c.515delT | p.Val172GlyfsTer20 | p.V172Gfs*20 | Q8TDX6 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| CSGALNACT1 | SNV | Missense_Mutation | novel | c.5N>C | p.Met2Thr | p.M2T | Q8TDX6 | protein_coding | tolerated_low_confidence(0.18) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CSGALNACT1 | SNV | Missense_Mutation | rs745624023 | c.178N>A | p.Val60Ile | p.V60I | Q8TDX6 | protein_coding | tolerated(0.24) | benign(0) | TCGA-C5-A1BM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| CSGALNACT1 | SNV | Missense_Mutation | c.728G>C | p.Arg243Pro | p.R243P | Q8TDX6 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| CSGALNACT1 | SNV | Missense_Mutation | novel | c.588N>C | p.Glu196Asp | p.E196D | Q8TDX6 | protein_coding | tolerated(0.31) | benign(0.013) | TCGA-VS-A9U7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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