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Gene: RAVER2 |
Gene summary for RAVER2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RAVER2 | Gene ID | 55225 |
Gene name | ribonucleoprotein, PTB binding 2 | |
Gene Alias | RAVER2 | |
Cytomap | 1p31.3 | |
Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q9HCJ3 |
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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 |
55225 | RAVER2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.06e-14 | -5.90e-01 | 0.0155 |
55225 | RAVER2 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.75e-02 | -2.19e-01 | -0.1464 |
55225 | RAVER2 | HTA11_866_3004761011 | Human | Colorectum | AD | 7.55e-11 | -5.85e-01 | 0.096 |
55225 | RAVER2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.84e-14 | -5.28e-01 | 0.0674 |
55225 | RAVER2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.92e-03 | -3.49e-01 | 0.294 |
55225 | RAVER2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 7.98e-04 | -3.38e-01 | 0.3859 |
55225 | RAVER2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 8.53e-05 | -6.09e-01 | 0.2585 |
55225 | RAVER2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.23e-21 | -6.13e-01 | 0.3005 |
55225 | RAVER2 | F007 | Human | Colorectum | FAP | 7.20e-03 | -3.79e-01 | 0.1176 |
55225 | RAVER2 | A001-C-207 | Human | Colorectum | FAP | 3.88e-07 | -4.13e-01 | 0.1278 |
55225 | RAVER2 | A015-C-203 | Human | Colorectum | FAP | 1.44e-30 | -5.04e-01 | -0.1294 |
55225 | RAVER2 | A015-C-204 | Human | Colorectum | FAP | 1.91e-06 | -3.53e-01 | -0.0228 |
55225 | RAVER2 | A014-C-040 | Human | Colorectum | FAP | 8.39e-04 | -2.87e-01 | -0.1184 |
55225 | RAVER2 | A002-C-201 | Human | Colorectum | FAP | 3.50e-16 | -4.32e-01 | 0.0324 |
55225 | RAVER2 | A002-C-203 | Human | Colorectum | FAP | 4.42e-05 | -2.05e-01 | 0.2786 |
55225 | RAVER2 | A001-C-119 | Human | Colorectum | FAP | 8.17e-15 | -6.41e-01 | -0.1557 |
55225 | RAVER2 | A001-C-108 | Human | Colorectum | FAP | 6.75e-21 | -3.87e-01 | -0.0272 |
55225 | RAVER2 | A002-C-205 | Human | Colorectum | FAP | 1.76e-23 | -5.65e-01 | -0.1236 |
55225 | RAVER2 | A001-C-104 | Human | Colorectum | FAP | 1.57e-06 | -3.27e-01 | 0.0184 |
55225 | RAVER2 | A015-C-005 | Human | Colorectum | FAP | 1.20e-07 | -3.78e-01 | -0.0336 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
GO:1903311 | Colorectum | AD | regulation of mRNA metabolic process | 117/3918 | 288/18723 | 1.69e-14 | 4.23e-12 | 117 |
GO:0043484 | Colorectum | AD | regulation of RNA splicing | 70/3918 | 148/18723 | 6.47e-13 | 1.16e-10 | 70 |
GO:0048024 | Colorectum | AD | regulation of mRNA splicing, via spliceosome | 50/3918 | 101/18723 | 1.62e-10 | 1.56e-08 | 50 |
GO:0050684 | Colorectum | AD | regulation of mRNA processing | 61/3918 | 137/18723 | 4.23e-10 | 3.58e-08 | 61 |
GO:0000380 | Colorectum | AD | alternative mRNA splicing, via spliceosome | 33/3918 | 77/18723 | 1.13e-05 | 2.55e-04 | 33 |
GO:0000381 | Colorectum | AD | regulation of alternative mRNA splicing, via spliceosome | 27/3918 | 60/18723 | 2.41e-05 | 4.66e-04 | 27 |
GO:00083802 | Colorectum | MSS | RNA splicing | 159/3467 | 434/18723 | 1.75e-19 | 1.22e-16 | 159 |
GO:19033112 | Colorectum | MSS | regulation of mRNA metabolic process | 115/3467 | 288/18723 | 1.23e-17 | 6.41e-15 | 115 |
GO:00003772 | Colorectum | MSS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
GO:00003982 | Colorectum | MSS | mRNA splicing, via spliceosome | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
GO:00003752 | Colorectum | MSS | RNA splicing, via transesterification reactions | 122/3467 | 324/18723 | 2.75e-16 | 8.58e-14 | 122 |
GO:00434842 | Colorectum | MSS | regulation of RNA splicing | 66/3467 | 148/18723 | 2.44e-13 | 5.25e-11 | 66 |
GO:00506842 | Colorectum | MSS | regulation of mRNA processing | 57/3467 | 137/18723 | 2.88e-10 | 2.68e-08 | 57 |
GO:00480242 | Colorectum | MSS | regulation of mRNA splicing, via spliceosome | 46/3467 | 101/18723 | 4.20e-10 | 3.49e-08 | 46 |
GO:00003802 | Colorectum | MSS | alternative mRNA splicing, via spliceosome | 33/3467 | 77/18723 | 6.87e-07 | 2.48e-05 | 33 |
GO:00003812 | Colorectum | MSS | regulation of alternative mRNA splicing, via spliceosome | 26/3467 | 60/18723 | 8.01e-06 | 2.03e-04 | 26 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
RAVER2 | SNV | Missense_Mutation | novel | c.1395A>C | p.Gln465His | p.Q465H | Q9HCJ3 | protein_coding | tolerated(0.21) | possibly_damaging(0.655) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
RAVER2 | SNV | Missense_Mutation | rs752817197 | c.941N>A | p.Arg314Gln | p.R314Q | Q9HCJ3 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RAVER2 | SNV | Missense_Mutation | c.251N>C | p.Glu84Ala | p.E84A | Q9HCJ3 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RAVER2 | SNV | Missense_Mutation | c.956N>A | p.Ala319Glu | p.A319E | Q9HCJ3 | protein_coding | deleterious(0) | possibly_damaging(0.876) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
RAVER2 | SNV | Missense_Mutation | rs865833350 | c.311N>A | p.Arg104Gln | p.R104Q | Q9HCJ3 | protein_coding | tolerated(0.26) | benign(0.292) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RAVER2 | SNV | Missense_Mutation | novel | c.894G>T | p.Lys298Asn | p.K298N | Q9HCJ3 | protein_coding | tolerated(0.19) | benign(0.037) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
RAVER2 | SNV | Missense_Mutation | novel | c.1799G>A | p.Ser600Asn | p.S600N | Q9HCJ3 | protein_coding | tolerated(1) | benign(0) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
RAVER2 | SNV | Missense_Mutation | novel | c.469G>A | p.Glu157Lys | p.E157K | Q9HCJ3 | protein_coding | deleterious(0.01) | benign(0.254) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
RAVER2 | SNV | Missense_Mutation | c.1370A>C | p.Lys457Thr | p.K457T | Q9HCJ3 | protein_coding | tolerated(0.14) | possibly_damaging(0.724) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
RAVER2 | SNV | Missense_Mutation | novel | c.795N>T | p.Gln265His | p.Q265H | Q9HCJ3 | protein_coding | tolerated(0.13) | probably_damaging(0.971) | TCGA-B5-A3FA-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 |
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