|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: GLYCTK |
Gene summary for GLYCTK |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GLYCTK | Gene ID | 132158 |
| Gene name | glycerate kinase | |
| Gene Alias | HBEBP2 | |
| Cytomap | 3p21.2 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | Q8IVS8 |
Top |
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 |
| 132158 | GLYCTK | NAFLD1 | Human | Liver | NAFLD | 1.62e-04 | 4.85e-01 | -0.04 |
| 132158 | GLYCTK | S43 | Human | Liver | Cirrhotic | 1.05e-02 | -4.78e-02 | -0.0187 |
| 132158 | GLYCTK | HCC1_Meng | Human | Liver | HCC | 3.91e-79 | 2.82e-01 | 0.0246 |
| 132158 | GLYCTK | HCC2_Meng | Human | Liver | HCC | 1.06e-02 | -1.09e-01 | 0.0107 |
| 132158 | GLYCTK | HCC2 | Human | Liver | HCC | 2.53e-29 | 5.19e+00 | 0.5341 |
| 132158 | GLYCTK | Pt14.b | Human | Liver | HCC | 4.32e-06 | 3.57e-01 | 0.018 |
| 132158 | GLYCTK | S014 | Human | Liver | HCC | 2.56e-15 | 6.32e-01 | 0.2254 |
| 132158 | GLYCTK | S015 | Human | Liver | HCC | 2.25e-18 | 9.81e-01 | 0.2375 |
| 132158 | GLYCTK | S016 | Human | Liver | HCC | 2.96e-20 | 6.49e-01 | 0.2243 |
| 132158 | GLYCTK | S027 | Human | Liver | HCC | 5.29e-03 | 4.77e-01 | 0.2446 |
| 132158 | GLYCTK | S028 | Human | Liver | HCC | 1.15e-18 | 7.79e-01 | 0.2503 |
| 132158 | GLYCTK | S029 | Human | Liver | HCC | 8.19e-16 | 8.96e-01 | 0.2581 |
| 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. |
Top |
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:00442825 | Liver | NAFLD | small molecule catabolic process | 91/1882 | 376/18723 | 8.96e-16 | 1.31e-12 | 91 |
| GO:00059965 | Liver | NAFLD | monosaccharide metabolic process | 53/1882 | 257/18723 | 2.89e-07 | 1.92e-05 | 53 |
| GO:00193185 | Liver | NAFLD | hexose metabolic process | 49/1882 | 237/18723 | 7.41e-07 | 4.12e-05 | 49 |
| GO:00160526 | Liver | NAFLD | carbohydrate catabolic process | 32/1882 | 154/18723 | 5.29e-05 | 1.21e-03 | 32 |
| GO:00060002 | Liver | NAFLD | fructose metabolic process | 5/1882 | 13/18723 | 6.58e-03 | 4.69e-02 | 5 |
| GO:004428211 | Liver | Cirrhotic | small molecule catabolic process | 151/4634 | 376/18723 | 2.20e-11 | 1.34e-09 | 151 |
| GO:000599612 | Liver | Cirrhotic | monosaccharide metabolic process | 104/4634 | 257/18723 | 1.74e-08 | 6.32e-07 | 104 |
| GO:001931812 | Liver | Cirrhotic | hexose metabolic process | 97/4634 | 237/18723 | 2.67e-08 | 9.16e-07 | 97 |
| GO:001605212 | Liver | Cirrhotic | carbohydrate catabolic process | 66/4634 | 154/18723 | 6.10e-07 | 1.32e-05 | 66 |
| GO:00060815 | Liver | Cirrhotic | cellular aldehyde metabolic process | 28/4634 | 60/18723 | 1.83e-04 | 1.71e-03 | 28 |
| GO:000599621 | Liver | HCC | monosaccharide metabolic process | 167/7958 | 257/18723 | 2.31e-13 | 1.25e-11 | 167 |
| GO:001931821 | Liver | HCC | hexose metabolic process | 155/7958 | 237/18723 | 7.63e-13 | 3.90e-11 | 155 |
| GO:004428221 | Liver | HCC | small molecule catabolic process | 225/7958 | 376/18723 | 6.50e-12 | 2.80e-10 | 225 |
| GO:001605222 | Liver | HCC | carbohydrate catabolic process | 99/7958 | 154/18723 | 3.79e-08 | 8.30e-07 | 99 |
| GO:000608112 | Liver | HCC | cellular aldehyde metabolic process | 39/7958 | 60/18723 | 3.61e-04 | 2.50e-03 | 39 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0120010 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa0120011 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa0120021 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
| hsa006304 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
| hsa00260 | Liver | Cirrhotic | Glycine, serine and threonine metabolism | 22/2530 | 40/8465 | 7.85e-04 | 4.51e-03 | 2.78e-03 | 22 |
| hsa00030 | Liver | Cirrhotic | Pentose phosphate pathway | 16/2530 | 30/8465 | 6.04e-03 | 2.12e-02 | 1.30e-02 | 16 |
| hsa0120031 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
| hsa0063011 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
| hsa002601 | Liver | Cirrhotic | Glycine, serine and threonine metabolism | 22/2530 | 40/8465 | 7.85e-04 | 4.51e-03 | 2.78e-03 | 22 |
| hsa000301 | Liver | Cirrhotic | Pentose phosphate pathway | 16/2530 | 30/8465 | 6.04e-03 | 2.12e-02 | 1.30e-02 | 16 |
| hsa0120041 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa0063021 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
| hsa002602 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
| hsa005615 | Liver | HCC | Glycerolipid metabolism | 41/4020 | 63/8465 | 3.59e-03 | 1.12e-02 | 6.22e-03 | 41 |
| hsa000302 | Liver | HCC | Pentose phosphate pathway | 21/4020 | 30/8465 | 1.06e-02 | 2.71e-02 | 1.51e-02 | 21 |
| hsa0120051 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa0063031 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
| hsa002603 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
| hsa0056112 | Liver | HCC | Glycerolipid metabolism | 41/4020 | 63/8465 | 3.59e-03 | 1.12e-02 | 6.22e-03 | 41 |
| hsa000303 | Liver | HCC | Pentose phosphate pathway | 21/4020 | 30/8465 | 1.06e-02 | 2.71e-02 | 1.51e-02 | 21 |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| GLYCTK | SNV | Missense_Mutation | novel | c.1123N>A | p.His375Asn | p.H375N | Q8IVS8 | protein_coding | tolerated(0.34) | benign(0) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GLYCTK | SNV | Missense_Mutation | c.1554N>C | p.Leu518Phe | p.L518F | Q8IVS8 | protein_coding | deleterious(0.01) | benign(0.378) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| GLYCTK | SNV | Missense_Mutation | c.845G>A | p.Arg282His | p.R282H | Q8IVS8 | protein_coding | deleterious(0.04) | benign(0.012) | TCGA-AR-A1AP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| GLYCTK | SNV | Missense_Mutation | c.440N>A | p.Pro147Gln | p.P147Q | Q8IVS8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-FU-A23L-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| GLYCTK | SNV | Missense_Mutation | c.1198N>A | p.Gly400Ser | p.G400S | Q8IVS8 | protein_coding | tolerated(0.18) | benign(0.001) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| GLYCTK | SNV | Missense_Mutation | rs761902954 | c.1072C>T | p.Arg358Cys | p.R358C | Q8IVS8 | protein_coding | tolerated(0.18) | benign(0.001) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
| GLYCTK | SNV | Missense_Mutation | rs769693391 | c.1265N>A | p.Arg422Gln | p.R422Q | Q8IVS8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AG-A02N-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | folinic | CR |
| GLYCTK | SNV | Missense_Mutation | rs762933911 | c.1202N>T | p.Pro401Leu | p.P401L | Q8IVS8 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GLYCTK | SNV | Missense_Mutation | novel | c.305N>A | p.Gly102Asp | p.G102D | Q8IVS8 | protein_coding | deleterious(0.01) | possibly_damaging(0.619) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| GLYCTK | SNV | Missense_Mutation | novel | c.1073N>A | p.Arg358His | p.R358H | Q8IVS8 | protein_coding | tolerated(0.56) | benign(0.001) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |