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Gene: RBP2 |
Gene summary for RBP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RBP2 | Gene ID | 5948 |
| Gene name | retinol binding protein 2 | |
| Gene Alias | CRABP-II | |
| Cytomap | 3q23 | |
| Gene Type | protein-coding | GO ID | GO:0001523 | UniProtAcc | P50120 |
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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 |
| 5948 | RBP2 | Pat01-B | Human | Stomach | GC | 3.24e-87 | 1.87e+00 | 0.5754 |
| 5948 | RBP2 | Pat02-B | Human | Stomach | GC | 8.23e-12 | 4.75e-01 | 0.0368 |
| 5948 | RBP2 | Pat03-B | Human | Stomach | GC | 5.13e-39 | 1.30e+00 | 0.3693 |
| 5948 | RBP2 | Pat04-B | Human | Stomach | GC | 2.32e-02 | 1.97e-01 | -0.1483 |
| 5948 | RBP2 | Pat05-B | Human | Stomach | GC | 6.46e-04 | 4.78e-01 | -0.0353 |
| 5948 | RBP2 | Pat17-B | Human | Stomach | GC | 1.69e-12 | 4.89e-01 | 0.3109 |
| 5948 | RBP2 | SIM_1 | Human | Stomach | SIM | 7.22e-36 | 1.08e+00 | 0.3573 |
| 5948 | RBP2 | SIM_4 | Human | Stomach | SIM | 2.45e-50 | 1.34e+00 | 0.2664 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia |
| ∗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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
| GO:0019058111 | Esophagus | ESCC | viral life cycle | 226/8552 | 317/18723 | 1.17e-20 | 1.76e-18 | 226 |
| GO:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| GO:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
| GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
| GO:001908017 | Esophagus | ESCC | viral gene expression | 80/8552 | 94/18723 | 2.04e-15 | 1.28e-13 | 80 |
| GO:0019079111 | Esophagus | ESCC | viral genome replication | 102/8552 | 131/18723 | 4.31e-14 | 2.19e-12 | 102 |
| GO:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
| GO:0050792111 | Esophagus | ESCC | regulation of viral process | 119/8552 | 164/18723 | 2.19e-12 | 9.03e-11 | 119 |
| GO:0010563111 | Esophagus | ESCC | negative regulation of phosphorus metabolic process | 274/8552 | 442/18723 | 2.32e-12 | 9.41e-11 | 274 |
| GO:0045936111 | Esophagus | ESCC | negative regulation of phosphate metabolic process | 273/8552 | 441/18723 | 3.18e-12 | 1.25e-10 | 273 |
| GO:0051348111 | Esophagus | ESCC | negative regulation of transferase activity | 177/8552 | 268/18723 | 1.08e-11 | 4.00e-10 | 177 |
| GO:1903900111 | Esophagus | ESCC | regulation of viral life cycle | 106/8552 | 148/18723 | 1.26e-10 | 3.72e-09 | 106 |
| GO:0042326111 | Esophagus | ESCC | negative regulation of phosphorylation | 237/8552 | 385/18723 | 1.86e-10 | 5.33e-09 | 237 |
| GO:0001933111 | Esophagus | ESCC | negative regulation of protein phosphorylation | 213/8552 | 342/18723 | 3.54e-10 | 9.76e-09 | 213 |
| GO:0045069110 | Esophagus | ESCC | regulation of viral genome replication | 67/8552 | 85/18723 | 3.81e-10 | 1.04e-08 | 67 |
| GO:00516075 | Esophagus | ESCC | defense response to virus | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| RBP2 | SNV | Missense_Mutation | novel | c.358C>G | p.Leu120Val | p.L120V | P50120 | protein_coding | deleterious(0.02) | benign(0.374) | TCGA-OL-A66P-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | CR |
| RBP2 | deletion | In_Frame_Del | novel | c.276_278delNNN | p.Val93del | p.V93del | P50120 | protein_coding | TCGA-A7-A6VW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | ||
| RBP2 | SNV | Missense_Mutation | c.106C>T | p.Arg36Cys | p.R36C | P50120 | protein_coding | tolerated(0.06) | benign(0.005) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| RBP2 | SNV | Missense_Mutation | c.85N>A | p.Ala29Thr | p.A29T | P50120 | protein_coding | tolerated(0.05) | benign(0.164) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD | |
| RBP2 | SNV | Missense_Mutation | rs117646086 | c.383N>A | p.Arg128His | p.R128H | P50120 | protein_coding | tolerated(0.17) | benign(0.001) | TCGA-DY-A1DF-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| RBP2 | SNV | Missense_Mutation | rs776742230 | c.190G>A | p.Asp64Asn | p.D64N | P50120 | protein_coding | tolerated(0.34) | benign(0.003) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RBP2 | SNV | Missense_Mutation | c.83N>C | p.Phe28Ser | p.F28S | P50120 | protein_coding | tolerated(0.07) | possibly_damaging(0.776) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| RBP2 | SNV | Missense_Mutation | rs371817821 | c.92N>A | p.Arg31His | p.R31H | P50120 | protein_coding | deleterious(0.03) | possibly_damaging(0.639) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RBP2 | SNV | Missense_Mutation | novel | c.20N>T | p.Gly7Val | p.G7V | P50120 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EO-A3AY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| RBP2 | SNV | Missense_Mutation | rs762979587 | c.68C>T | p.Ala23Val | p.A23V | P50120 | protein_coding | tolerated(0.07) | benign(0.176) | TCGA-EY-A1GD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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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