|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: RIDA |
Gene summary for RIDA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RIDA | Gene ID | 10247 |
| Gene name | reactive intermediate imine deaminase A homolog | |
| Gene Alias | HRSP12 | |
| Cytomap | 8q22.2 | |
| Gene Type | protein-coding | GO ID | GO:0001655 | UniProtAcc | A0A024R9H2 |
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 |
| 10247 | RIDA | NAFLD1 | Human | Liver | NAFLD | 7.90e-06 | 4.33e-01 | -0.04 |
| 10247 | RIDA | HCC1_Meng | Human | Liver | HCC | 4.58e-11 | -3.62e-01 | 0.0246 |
| 10247 | RIDA | HCC2_Meng | Human | Liver | HCC | 2.20e-10 | -3.62e-01 | 0.0107 |
| 10247 | RIDA | cirrhotic1 | Human | Liver | Cirrhotic | 4.58e-11 | -3.62e-01 | 0.0202 |
| 10247 | RIDA | cirrhotic2 | Human | Liver | Cirrhotic | 1.01e-10 | -3.62e-01 | 0.0201 |
| 10247 | RIDA | cirrhotic3 | Human | Liver | Cirrhotic | 3.31e-05 | -3.62e-01 | 0.0215 |
| 10247 | RIDA | HCC1 | Human | Liver | HCC | 1.23e-02 | 2.65e+00 | 0.5336 |
| 10247 | RIDA | HCC2 | Human | Liver | HCC | 1.49e-19 | 3.03e+00 | 0.5341 |
| 10247 | RIDA | Pt13.a | Human | Liver | HCC | 2.09e-11 | -3.62e-01 | 0.021 |
| 10247 | RIDA | Pt13.b | Human | Liver | HCC | 3.70e-04 | -3.62e-01 | 0.0251 |
| 10247 | RIDA | Pt14.d | Human | Liver | HCC | 4.58e-11 | -3.62e-01 | 0.0143 |
| 10247 | RIDA | S014 | Human | Liver | HCC | 6.92e-24 | 9.31e-01 | 0.2254 |
| 10247 | RIDA | S015 | Human | Liver | HCC | 7.41e-26 | 1.45e+00 | 0.2375 |
| 10247 | RIDA | S016 | Human | Liver | HCC | 2.09e-29 | 9.50e-01 | 0.2243 |
| 10247 | RIDA | S027 | Human | Liver | HCC | 1.95e-07 | 1.28e+00 | 0.2446 |
| 10247 | RIDA | S028 | Human | Liver | HCC | 1.84e-26 | 1.40e+00 | 0.2503 |
| 10247 | RIDA | S029 | Human | Liver | HCC | 3.75e-34 | 1.86e+00 | 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:190331321 | Liver | HCC | positive regulation of mRNA metabolic process | 85/7958 | 118/18723 | 7.10e-11 | 2.56e-09 | 85 |
| GO:00463952 | Liver | HCC | carboxylic acid catabolic process | 149/7958 | 236/18723 | 1.11e-10 | 3.87e-09 | 149 |
| GO:00905011 | Liver | HCC | RNA phosphodiester bond hydrolysis | 101/7958 | 152/18723 | 1.99e-09 | 5.63e-08 | 101 |
| GO:19016052 | Liver | HCC | alpha-amino acid metabolic process | 124/7958 | 195/18723 | 2.07e-09 | 5.79e-08 | 124 |
| GO:00065202 | Liver | HCC | cellular amino acid metabolic process | 167/7958 | 284/18723 | 1.91e-08 | 4.56e-07 | 167 |
| GO:005077921 | Liver | HCC | RNA destabilization | 63/7958 | 88/18723 | 2.99e-08 | 6.77e-07 | 63 |
| GO:006101421 | Liver | HCC | positive regulation of mRNA catabolic process | 62/7958 | 87/18723 | 5.08e-08 | 1.09e-06 | 62 |
| GO:006115721 | Liver | HCC | mRNA destabilization | 60/7958 | 84/18723 | 7.28e-08 | 1.48e-06 | 60 |
| GO:0090305 | Liver | HCC | nucleic acid phosphodiester bond hydrolysis | 152/7958 | 261/18723 | 1.90e-07 | 3.46e-06 | 152 |
| GO:00090632 | Liver | HCC | cellular amino acid catabolic process | 70/7958 | 110/18723 | 6.12e-06 | 7.52e-05 | 70 |
| GO:0090502 | Liver | HCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 52/7958 | 82/18723 | 1.06e-04 | 9.08e-04 | 52 |
| GO:00090692 | Liver | HCC | serine family amino acid metabolic process | 29/7958 | 40/18723 | 1.17e-04 | 9.87e-04 | 29 |
| GO:00090662 | Liver | HCC | aspartate family amino acid metabolic process | 34/7958 | 49/18723 | 1.28e-04 | 1.06e-03 | 34 |
| GO:003424921 | Liver | HCC | negative regulation of cellular amide metabolic process | 144/7958 | 273/18723 | 3.80e-04 | 2.61e-03 | 144 |
| GO:19016062 | Liver | HCC | alpha-amino acid catabolic process | 53/7958 | 87/18723 | 4.01e-04 | 2.71e-03 | 53 |
| GO:001714821 | Liver | HCC | negative regulation of translation | 129/7958 | 245/18723 | 8.14e-04 | 4.87e-03 | 129 |
| GO:00016553 | Liver | HCC | urogenital system development | 170/7958 | 338/18723 | 2.15e-03 | 1.08e-02 | 170 |
| GO:00018222 | Liver | HCC | kidney development | 148/7958 | 293/18723 | 3.25e-03 | 1.49e-02 | 148 |
| GO:00720012 | Liver | HCC | renal system development | 152/7958 | 302/18723 | 3.45e-03 | 1.56e-02 | 152 |
| GO:003032311 | Liver | HCC | respiratory tube development | 95/7958 | 181/18723 | 4.15e-03 | 1.81e-02 | 95 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| RIDA | SNV | Missense_Mutation | rs779193135 | c.359N>A | p.Arg120Gln | p.R120Q | P52758 | protein_coding | tolerated(0.23) | benign(0.098) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| RIDA | SNV | Missense_Mutation | c.59N>T | p.Pro20Leu | p.P20L | P52758 | protein_coding | deleterious(0.02) | probably_damaging(0.943) | TCGA-AA-3662-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | capecitabine | PR | |
| RIDA | SNV | Missense_Mutation | rs779193135 | c.359G>A | p.Arg120Gln | p.R120Q | P52758 | protein_coding | tolerated(0.23) | benign(0.098) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| RIDA | SNV | Missense_Mutation | rs779193135 | c.359N>A | p.Arg120Gln | p.R120Q | P52758 | protein_coding | tolerated(0.23) | benign(0.098) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RIDA | SNV | Missense_Mutation | c.212N>A | p.Cys71Tyr | p.C71Y | P52758 | protein_coding | tolerated(0.09) | benign(0.122) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RIDA | SNV | Missense_Mutation | rs779193135 | c.359N>A | p.Arg120Gln | p.R120Q | P52758 | protein_coding | tolerated(0.23) | benign(0.098) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RIDA | deletion | Frame_Shift_Del | novel | c.182delN | p.Asn61ThrfsTer6 | p.N61Tfs*6 | P52758 | protein_coding | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RIDA | SNV | Missense_Mutation | c.119N>G | p.Asp40Gly | p.D40G | P52758 | protein_coding | deleterious(0.01) | possibly_damaging(0.724) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| RIDA | SNV | Missense_Mutation | novel | c.113N>A | p.Gly38Asp | p.G38D | P52758 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| RIDA | SNV | Missense_Mutation | novel | c.244N>A | p.Leu82Ile | p.L82I | P52758 | protein_coding | deleterious(0.01) | probably_damaging(0.93) | TCGA-EY-A1GI-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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 |