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Gene: ST6GALNAC3 |
Gene summary for ST6GALNAC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ST6GALNAC3 | Gene ID | 256435 |
| Gene name | ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 | |
| Gene Alias | PRO7177 | |
| Cytomap | 1p31.1 | |
| Gene Type | protein-coding | GO ID | GO:0001573 | UniProtAcc | Q8NDV1 |
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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 |
| 256435 | ST6GALNAC3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.47e-13 | -5.98e-01 | 0.0155 |
| 256435 | ST6GALNAC3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.04e-02 | -4.90e-01 | -0.1808 |
| 256435 | ST6GALNAC3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.49e-06 | -6.15e-01 | -0.0811 |
| 256435 | ST6GALNAC3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.27e-02 | -5.11e-01 | -0.1207 |
| 256435 | ST6GALNAC3 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.10e-07 | -4.63e-01 | -0.1001 |
| 256435 | ST6GALNAC3 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.26e-10 | -5.91e-01 | 0.096 |
| 256435 | ST6GALNAC3 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.26e-05 | -5.75e-01 | 0.0338 |
| 256435 | ST6GALNAC3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 4.46e-08 | -4.77e-01 | 0.0674 |
| 256435 | ST6GALNAC3 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.93e-02 | -5.09e-01 | 0.0588 |
| 256435 | ST6GALNAC3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.30e-25 | -6.35e-01 | 0.294 |
| 256435 | ST6GALNAC3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.93e-06 | -6.29e-01 | 0.281 |
| 256435 | ST6GALNAC3 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.17e-05 | -6.63e-01 | 0.2585 |
| 256435 | ST6GALNAC3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.31e-23 | -6.31e-01 | 0.3005 |
| 256435 | ST6GALNAC3 | F007 | Human | Colorectum | FAP | 2.59e-08 | -6.17e-01 | 0.1176 |
| 256435 | ST6GALNAC3 | A002-C-010 | Human | Colorectum | FAP | 3.40e-11 | -4.92e-01 | 0.242 |
| 256435 | ST6GALNAC3 | A001-C-207 | Human | Colorectum | FAP | 2.87e-11 | -5.95e-01 | 0.1278 |
| 256435 | ST6GALNAC3 | A015-C-203 | Human | Colorectum | FAP | 1.18e-21 | -5.41e-01 | -0.1294 |
| 256435 | ST6GALNAC3 | A015-C-204 | Human | Colorectum | FAP | 5.20e-13 | -6.02e-01 | -0.0228 |
| 256435 | ST6GALNAC3 | A014-C-040 | Human | Colorectum | FAP | 1.56e-02 | -5.27e-01 | -0.1184 |
| 256435 | ST6GALNAC3 | A002-C-201 | Human | Colorectum | FAP | 6.07e-19 | -6.11e-01 | 0.0324 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:0016032 | Colorectum | AD | viral process | 168/3918 | 415/18723 | 4.67e-20 | 3.66e-17 | 168 |
| GO:0019080 | Colorectum | AD | viral gene expression | 42/3918 | 94/18723 | 1.90e-07 | 8.02e-06 | 42 |
| GO:0019082 | Colorectum | AD | viral protein processing | 17/3918 | 29/18723 | 1.04e-05 | 2.40e-04 | 17 |
| GO:0006486 | Colorectum | AD | protein glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
| GO:0043413 | Colorectum | AD | macromolecule glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
| GO:0070085 | Colorectum | AD | glycosylation | 67/3918 | 240/18723 | 5.78e-03 | 3.67e-02 | 67 |
| GO:00160321 | Colorectum | SER | viral process | 118/2897 | 415/18723 | 8.36e-12 | 1.65e-09 | 118 |
| GO:00190801 | Colorectum | SER | viral gene expression | 29/2897 | 94/18723 | 1.32e-04 | 2.66e-03 | 29 |
| GO:00160322 | Colorectum | MSS | viral process | 157/3467 | 415/18723 | 7.94e-21 | 6.19e-18 | 157 |
| GO:00190802 | Colorectum | MSS | viral gene expression | 41/3467 | 94/18723 | 1.74e-08 | 9.85e-07 | 41 |
| GO:00190821 | Colorectum | MSS | viral protein processing | 17/3467 | 29/18723 | 1.81e-06 | 5.70e-05 | 17 |
| GO:00160324 | Colorectum | FAP | viral process | 114/2622 | 415/18723 | 3.00e-13 | 2.63e-10 | 114 |
| GO:00190804 | Colorectum | FAP | viral gene expression | 29/2622 | 94/18723 | 2.07e-05 | 5.05e-04 | 29 |
| GO:00190822 | Colorectum | FAP | viral protein processing | 11/2622 | 29/18723 | 1.20e-03 | 1.14e-02 | 11 |
| GO:00064861 | Colorectum | FAP | protein glycosylation | 48/2622 | 226/18723 | 1.85e-03 | 1.57e-02 | 48 |
| GO:00434131 | Colorectum | FAP | macromolecule glycosylation | 48/2622 | 226/18723 | 1.85e-03 | 1.57e-02 | 48 |
| GO:00700851 | Colorectum | FAP | glycosylation | 50/2622 | 240/18723 | 2.30e-03 | 1.85e-02 | 50 |
| GO:0009101 | Colorectum | FAP | glycoprotein biosynthetic process | 63/2622 | 317/18723 | 2.31e-03 | 1.86e-02 | 63 |
| GO:00160325 | Colorectum | CRC | viral process | 95/2078 | 415/18723 | 3.31e-12 | 3.30e-09 | 95 |
| GO:00190805 | Colorectum | CRC | viral gene expression | 26/2078 | 94/18723 | 7.43e-06 | 2.72e-04 | 26 |
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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 |
| ST6GALNAC3 | SNV | Missense_Mutation | novel | c.228C>A | p.Asp76Glu | p.D76E | Q8NDV1 | protein_coding | benign(0.103) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ST6GALNAC3 | SNV | Missense_Mutation | rs376599589 | c.421N>T | p.Asp141Tyr | p.D141Y | Q8NDV1 | protein_coding | benign(0.026) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| ST6GALNAC3 | SNV | Missense_Mutation | c.113A>G | p.Asn38Ser | p.N38S | Q8NDV1 | protein_coding | benign(0) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| ST6GALNAC3 | SNV | Missense_Mutation | c.272G>A | p.Gly91Asp | p.G91D | Q8NDV1 | protein_coding | possibly_damaging(0.612) | TCGA-E9-A1R0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||
| ST6GALNAC3 | insertion | Frame_Shift_Ins | novel | c.622_623insCAACTCGAATCAT | p.Arg208ThrfsTer37 | p.R208Tfs*37 | Q8NDV1 | protein_coding | TCGA-A1-A0SM-01 | Breast | breast invasive carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| ST6GALNAC3 | insertion | In_Frame_Ins | novel | c.414_415insGTC | p.Lys138_Asn139insVal | p.K138_N139insV | Q8NDV1 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| ST6GALNAC3 | insertion | Frame_Shift_Ins | novel | c.415_416insAGTTTTTTTCAAAAGTTTTATCTTTG | p.Asn139LysfsTer32 | p.N139Kfs*32 | Q8NDV1 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| ST6GALNAC3 | SNV | Missense_Mutation | rs764007928 | c.77N>A | p.Arg26His | p.R26H | Q8NDV1 | protein_coding | benign(0) | TCGA-EX-A69M-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| ST6GALNAC3 | SNV | Missense_Mutation | rs373383533 | c.476G>A | p.Arg159His | p.R159H | Q8NDV1 | protein_coding | probably_damaging(0.97) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| ST6GALNAC3 | SNV | Missense_Mutation | c.305N>T | p.Ser102Phe | p.S102F | Q8NDV1 | protein_coding | probably_damaging(0.91) | TCGA-IR-A3LA-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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