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Gene: GYS2 |
Gene summary for GYS2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GYS2 | Gene ID | 2998 |
| Gene name | glycogen synthase 2 | |
| Gene Alias | GYS2 | |
| Cytomap | 12p12.1 | |
| Gene Type | protein-coding | GO ID | GO:0000271 | UniProtAcc | P54840 |
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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 |
| 2998 | GYS2 | NAFLD1 | Human | Liver | NAFLD | 7.44e-14 | 1.06e+00 | -0.04 |
| 2998 | GYS2 | S41 | Human | Liver | Cirrhotic | 2.52e-06 | 5.93e-01 | -0.0343 |
| 2998 | GYS2 | S43 | Human | Liver | Cirrhotic | 1.95e-02 | -2.31e-02 | -0.0187 |
| 2998 | GYS2 | HCC1_Meng | Human | Liver | HCC | 1.08e-04 | -1.24e-01 | 0.0246 |
| 2998 | GYS2 | HCC2_Meng | Human | Liver | HCC | 2.24e-05 | -1.30e-01 | 0.0107 |
| 2998 | GYS2 | cirrhotic1 | Human | Liver | Cirrhotic | 1.02e-04 | -1.30e-01 | 0.0202 |
| 2998 | GYS2 | cirrhotic2 | Human | Liver | Cirrhotic | 4.47e-03 | -1.28e-01 | 0.0201 |
| 2998 | GYS2 | Pt13.a | Human | Liver | HCC | 3.60e-02 | -1.12e-01 | 0.021 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00060917 | Liver | NAFLD | generation of precursor metabolites and energy | 84/1882 | 490/18723 | 7.03e-07 | 3.95e-05 | 84 |
| GO:00442623 | Liver | NAFLD | cellular carbohydrate metabolic process | 55/1882 | 283/18723 | 1.27e-06 | 6.01e-05 | 55 |
| GO:0016051 | Liver | NAFLD | carbohydrate biosynthetic process | 43/1882 | 202/18723 | 1.55e-06 | 6.96e-05 | 43 |
| GO:0034637 | Liver | NAFLD | cellular carbohydrate biosynthetic process | 20/1882 | 78/18723 | 6.46e-05 | 1.39e-03 | 20 |
| GO:00097437 | Liver | NAFLD | response to carbohydrate | 45/1882 | 253/18723 | 1.07e-04 | 2.11e-03 | 45 |
| GO:0005976 | Liver | NAFLD | polysaccharide metabolic process | 24/1882 | 107/18723 | 1.28e-04 | 2.46e-03 | 24 |
| GO:0044264 | Liver | NAFLD | cellular polysaccharide metabolic process | 22/1882 | 96/18723 | 1.73e-04 | 3.08e-03 | 22 |
| GO:0005977 | Liver | NAFLD | glycogen metabolic process | 18/1882 | 72/18723 | 2.09e-04 | 3.60e-03 | 18 |
| GO:0006073 | Liver | NAFLD | cellular glucan metabolic process | 18/1882 | 73/18723 | 2.51e-04 | 4.12e-03 | 18 |
| GO:0044042 | Liver | NAFLD | glucan metabolic process | 18/1882 | 73/18723 | 2.51e-04 | 4.12e-03 | 18 |
| GO:0000271 | Liver | NAFLD | polysaccharide biosynthetic process | 17/1882 | 72/18723 | 6.35e-04 | 8.27e-03 | 17 |
| GO:0006112 | Liver | NAFLD | energy reserve metabolic process | 18/1882 | 84/18723 | 1.49e-03 | 1.64e-02 | 18 |
| GO:0033692 | Liver | NAFLD | cellular polysaccharide biosynthetic process | 15/1882 | 65/18723 | 1.66e-03 | 1.74e-02 | 15 |
| GO:00342847 | Liver | NAFLD | response to monosaccharide | 37/1882 | 225/18723 | 1.86e-03 | 1.91e-02 | 37 |
| GO:00097467 | Liver | NAFLD | response to hexose | 36/1882 | 219/18723 | 2.14e-03 | 2.08e-02 | 36 |
| GO:00159807 | Liver | NAFLD | energy derivation by oxidation of organic compounds | 48/1882 | 318/18723 | 2.78e-03 | 2.54e-02 | 48 |
| GO:0005978 | Liver | NAFLD | glycogen biosynthetic process | 11/1882 | 44/18723 | 3.45e-03 | 2.98e-02 | 11 |
| GO:0009250 | Liver | NAFLD | glucan biosynthetic process | 11/1882 | 44/18723 | 3.45e-03 | 2.98e-02 | 11 |
| GO:000609112 | Liver | Cirrhotic | generation of precursor metabolites and energy | 238/4634 | 490/18723 | 6.85e-31 | 1.07e-27 | 238 |
| GO:001598012 | Liver | Cirrhotic | energy derivation by oxidation of organic compounds | 154/4634 | 318/18723 | 3.11e-20 | 8.87e-18 | 154 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa049316 | Liver | NAFLD | Insulin resistance | 29/1043 | 108/8465 | 3.01e-05 | 7.59e-04 | 6.11e-04 | 29 |
| hsa041528 | Liver | NAFLD | AMPK signaling pathway | 28/1043 | 121/8465 | 6.26e-04 | 9.78e-03 | 7.88e-03 | 28 |
| hsa049106 | Liver | NAFLD | Insulin signaling pathway | 29/1043 | 137/8465 | 2.23e-03 | 2.46e-02 | 1.99e-02 | 29 |
| hsa0492210 | Liver | NAFLD | Glucagon signaling pathway | 24/1043 | 107/8465 | 2.33e-03 | 2.46e-02 | 1.99e-02 | 24 |
| hsa0493111 | Liver | NAFLD | Insulin resistance | 29/1043 | 108/8465 | 3.01e-05 | 7.59e-04 | 6.11e-04 | 29 |
| hsa0415211 | Liver | NAFLD | AMPK signaling pathway | 28/1043 | 121/8465 | 6.26e-04 | 9.78e-03 | 7.88e-03 | 28 |
| hsa0491011 | Liver | NAFLD | Insulin signaling pathway | 29/1043 | 137/8465 | 2.23e-03 | 2.46e-02 | 1.99e-02 | 29 |
| hsa0492211 | Liver | NAFLD | Glucagon signaling pathway | 24/1043 | 107/8465 | 2.33e-03 | 2.46e-02 | 1.99e-02 | 24 |
| hsa0541514 | Liver | Cirrhotic | Diabetic cardiomyopathy | 108/2530 | 203/8465 | 1.99e-12 | 4.41e-11 | 2.72e-11 | 108 |
| hsa0491021 | Liver | Cirrhotic | Insulin signaling pathway | 56/2530 | 137/8465 | 3.74e-03 | 1.50e-02 | 9.26e-03 | 56 |
| hsa0415221 | Liver | Cirrhotic | AMPK signaling pathway | 49/2530 | 121/8465 | 7.90e-03 | 2.74e-02 | 1.69e-02 | 49 |
| hsa0492221 | Liver | Cirrhotic | Glucagon signaling pathway | 43/2530 | 107/8465 | 1.42e-02 | 4.35e-02 | 2.68e-02 | 43 |
| hsa0541515 | Liver | Cirrhotic | Diabetic cardiomyopathy | 108/2530 | 203/8465 | 1.99e-12 | 4.41e-11 | 2.72e-11 | 108 |
| hsa0491031 | Liver | Cirrhotic | Insulin signaling pathway | 56/2530 | 137/8465 | 3.74e-03 | 1.50e-02 | 9.26e-03 | 56 |
| hsa0415231 | Liver | Cirrhotic | AMPK signaling pathway | 49/2530 | 121/8465 | 7.90e-03 | 2.74e-02 | 1.69e-02 | 49 |
| hsa0492231 | Liver | Cirrhotic | Glucagon signaling pathway | 43/2530 | 107/8465 | 1.42e-02 | 4.35e-02 | 2.68e-02 | 43 |
| hsa0541522 | Liver | HCC | Diabetic cardiomyopathy | 151/4020 | 203/8465 | 2.72e-15 | 1.01e-13 | 5.63e-14 | 151 |
| hsa0491041 | Liver | HCC | Insulin signaling pathway | 95/4020 | 137/8465 | 1.53e-07 | 1.97e-06 | 1.10e-06 | 95 |
| hsa0493121 | Liver | HCC | Insulin resistance | 77/4020 | 108/8465 | 3.89e-07 | 4.46e-06 | 2.48e-06 | 77 |
| hsa0415241 | Liver | HCC | AMPK signaling pathway | 77/4020 | 121/8465 | 2.32e-04 | 1.11e-03 | 6.18e-04 | 77 |
| Page: 1 2 |
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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 |
| GYS2 | SNV | Missense_Mutation | novel | c.1289G>C | p.Arg430Thr | p.R430T | P54840 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| GYS2 | SNV | Missense_Mutation | c.1243G>A | p.Asp415Asn | p.D415N | P54840 | protein_coding | tolerated(0.18) | probably_damaging(0.991) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GYS2 | SNV | Missense_Mutation | rs767722149 | c.841N>A | p.Gly281Ser | p.G281S | P54840 | protein_coding | deleterious(0.01) | probably_damaging(0.992) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| GYS2 | SNV | Missense_Mutation | c.1552G>C | p.Glu518Gln | p.E518Q | P54840 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| GYS2 | SNV | Missense_Mutation | c.1320N>T | p.Leu440Phe | p.L440F | P54840 | protein_coding | tolerated(0.11) | benign(0.06) | TCGA-JW-A5VH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
| GYS2 | SNV | Missense_Mutation | c.966N>T | p.Lys322Asn | p.K322N | P54840 | protein_coding | tolerated(0.53) | benign(0.084) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD | |
| GYS2 | SNV | Missense_Mutation | c.1336N>T | p.His446Tyr | p.H446Y | P54840 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD | |
| GYS2 | SNV | Missense_Mutation | c.183N>T | p.Glu61Asp | p.E61D | P54840 | protein_coding | tolerated(1) | benign(0.005) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| GYS2 | SNV | Missense_Mutation | c.78N>T | p.Glu26Asp | p.E26D | P54840 | protein_coding | tolerated(0.12) | benign(0.001) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| GYS2 | SNV | Missense_Mutation | novel | c.1150G>A | p.Ala384Thr | p.A384T | P54840 | protein_coding | deleterious(0) | possibly_damaging(0.902) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| Page: 1 |
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