|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: GCDH |
Gene summary for GCDH |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GCDH | Gene ID | 2639 |
| Gene name | glutaryl-CoA dehydrogenase | |
| Gene Alias | ACAD5 | |
| Cytomap | 19p13.13 | |
| Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | A0A024R7F9 |
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 |
| 2639 | GCDH | LZE4T | Human | Esophagus | ESCC | 1.86e-03 | 1.37e-01 | 0.0811 |
| 2639 | GCDH | LZE7T | Human | Esophagus | ESCC | 1.02e-05 | 3.53e-01 | 0.0667 |
| 2639 | GCDH | LZE24T | Human | Esophagus | ESCC | 4.44e-12 | 2.96e-01 | 0.0596 |
| 2639 | GCDH | LZE21T | Human | Esophagus | ESCC | 2.86e-03 | 4.03e-01 | 0.0655 |
| 2639 | GCDH | P1T-E | Human | Esophagus | ESCC | 8.15e-08 | 4.02e-01 | 0.0875 |
| 2639 | GCDH | P2T-E | Human | Esophagus | ESCC | 1.97e-11 | 2.32e-01 | 0.1177 |
| 2639 | GCDH | P4T-E | Human | Esophagus | ESCC | 1.99e-20 | 4.67e-01 | 0.1323 |
| 2639 | GCDH | P5T-E | Human | Esophagus | ESCC | 6.84e-11 | 2.18e-01 | 0.1327 |
| 2639 | GCDH | P8T-E | Human | Esophagus | ESCC | 1.38e-23 | 3.55e-01 | 0.0889 |
| 2639 | GCDH | P9T-E | Human | Esophagus | ESCC | 1.37e-13 | 3.27e-01 | 0.1131 |
| 2639 | GCDH | P10T-E | Human | Esophagus | ESCC | 1.65e-28 | 4.53e-01 | 0.116 |
| 2639 | GCDH | P11T-E | Human | Esophagus | ESCC | 2.29e-12 | 4.57e-01 | 0.1426 |
| 2639 | GCDH | P12T-E | Human | Esophagus | ESCC | 1.98e-25 | 5.00e-01 | 0.1122 |
| 2639 | GCDH | P15T-E | Human | Esophagus | ESCC | 1.83e-10 | 2.75e-01 | 0.1149 |
| 2639 | GCDH | P16T-E | Human | Esophagus | ESCC | 1.39e-21 | 3.05e-01 | 0.1153 |
| 2639 | GCDH | P17T-E | Human | Esophagus | ESCC | 1.70e-08 | 4.10e-01 | 0.1278 |
| 2639 | GCDH | P19T-E | Human | Esophagus | ESCC | 4.67e-06 | 5.78e-01 | 0.1662 |
| 2639 | GCDH | P20T-E | Human | Esophagus | ESCC | 1.41e-12 | 2.90e-01 | 0.1124 |
| 2639 | GCDH | P21T-E | Human | Esophagus | ESCC | 1.46e-22 | 4.49e-01 | 0.1617 |
| 2639 | GCDH | P22T-E | Human | Esophagus | ESCC | 2.02e-20 | 3.89e-01 | 0.1236 |
| Page: 1 2 3 4 |
| 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. |
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:0006753110 | Esophagus | ESCC | nucleoside phosphate metabolic process | 288/8552 | 497/18723 | 1.80e-08 | 3.50e-07 | 288 |
| GO:0019693111 | Esophagus | ESCC | ribose phosphate metabolic process | 234/8552 | 396/18723 | 4.24e-08 | 7.76e-07 | 234 |
| GO:0009117111 | Esophagus | ESCC | nucleotide metabolic process | 282/8552 | 489/18723 | 4.70e-08 | 8.50e-07 | 282 |
| GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:0009259111 | Esophagus | ESCC | ribonucleotide metabolic process | 224/8552 | 385/18723 | 4.41e-07 | 6.00e-06 | 224 |
| GO:0072521111 | Esophagus | ESCC | purine-containing compound metabolic process | 238/8552 | 416/18723 | 1.20e-06 | 1.49e-05 | 238 |
| GO:0009150111 | Esophagus | ESCC | purine ribonucleotide metabolic process | 213/8552 | 368/18723 | 1.40e-06 | 1.69e-05 | 213 |
| GO:0046390110 | Esophagus | ESCC | ribose phosphate biosynthetic process | 119/8552 | 190/18723 | 1.73e-06 | 2.06e-05 | 119 |
| GO:00442725 | Esophagus | ESCC | sulfur compound biosynthetic process | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
| GO:0006163111 | Esophagus | ESCC | purine nucleotide metabolic process | 226/8552 | 396/18723 | 2.81e-06 | 3.21e-05 | 226 |
| GO:00193958 | Esophagus | ESCC | fatty acid oxidation | 69/8552 | 103/18723 | 9.95e-06 | 9.44e-05 | 69 |
| GO:000916516 | Esophagus | ESCC | nucleotide biosynthetic process | 150/8552 | 254/18723 | 1.12e-05 | 1.06e-04 | 150 |
| GO:0009260110 | Esophagus | ESCC | ribonucleotide biosynthetic process | 112/8552 | 182/18723 | 1.12e-05 | 1.06e-04 | 112 |
| GO:190129316 | Esophagus | ESCC | nucleoside phosphate biosynthetic process | 151/8552 | 256/18723 | 1.15e-05 | 1.08e-04 | 151 |
| GO:00338664 | Esophagus | ESCC | nucleoside bisphosphate biosynthetic process | 44/8552 | 60/18723 | 1.25e-05 | 1.15e-04 | 44 |
| GO:00340304 | Esophagus | ESCC | ribonucleoside bisphosphate biosynthetic process | 44/8552 | 60/18723 | 1.25e-05 | 1.15e-04 | 44 |
| GO:00340334 | Esophagus | ESCC | purine nucleoside bisphosphate biosynthetic process | 44/8552 | 60/18723 | 1.25e-05 | 1.15e-04 | 44 |
| GO:00344407 | Esophagus | ESCC | lipid oxidation | 71/8552 | 108/18723 | 2.00e-05 | 1.74e-04 | 71 |
| GO:007252217 | Esophagus | ESCC | purine-containing compound biosynthetic process | 120/8552 | 200/18723 | 3.02e-05 | 2.51e-04 | 120 |
| GO:00090628 | Esophagus | ESCC | fatty acid catabolic process | 66/8552 | 100/18723 | 3.21e-05 | 2.66e-04 | 66 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0031010 | Esophagus | ESCC | Lysine degradation | 41/4205 | 63/8465 | 9.63e-03 | 2.27e-02 | 1.16e-02 | 41 |
| hsa0031013 | Esophagus | ESCC | Lysine degradation | 41/4205 | 63/8465 | 9.63e-03 | 2.27e-02 | 1.16e-02 | 41 |
| 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 |
| GCDH | SNV | Missense_Mutation | c.773N>T | p.Ala258Val | p.A258V | Q92947 | protein_coding | deleterious_low_confidence(0) | benign(0.442) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GCDH | SNV | Missense_Mutation | c.233G>C | p.Arg78Thr | p.R78T | Q92947 | protein_coding | deleterious_low_confidence(0.01) | benign(0.093) | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | |
| GCDH | insertion | Nonsense_Mutation | novel | c.616_617insCTTAGCTGGGCAGGGCCCTGTTCTCTATTGTCCTGCTT | p.Leu206ProfsTer2 | p.L206Pfs*2 | Q92947 | protein_coding | TCGA-A8-A09K-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| GCDH | SNV | Missense_Mutation | rs759176685 | c.1009G>T | p.Ala337Ser | p.A337S | Q92947 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.985) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| GCDH | SNV | Missense_Mutation | c.1171N>A | p.Gly391Arg | p.G391R | Q92947 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.999) | TCGA-FU-A23L-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| GCDH | SNV | Missense_Mutation | rs201509112 | c.1210N>A | p.Ala404Thr | p.A404T | Q92947 | protein_coding | deleterious_low_confidence(0.02) | benign(0.025) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GCDH | SNV | Missense_Mutation | c.1060G>T | p.Gly354Cys | p.G354C | Q92947 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.999) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| GCDH | SNV | Missense_Mutation | novel | c.739N>T | p.Ala247Ser | p.A247S | Q92947 | protein_coding | deleterious_low_confidence(0.03) | benign(0.167) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GCDH | SNV | Missense_Mutation | rs748275416 | c.1064N>A | p.Arg355His | p.R355H | Q92947 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.733) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
| GCDH | SNV | Missense_Mutation | c.1174N>G | p.Asn392Asp | p.N392D | Q92947 | protein_coding | deleterious_low_confidence(0) | probably_damaging(1) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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 |