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Gene: RTN4RL2 |
Gene summary for RTN4RL2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RTN4RL2 | Gene ID | 349667 |
| Gene name | reticulon 4 receptor like 2 | |
| Gene Alias | NGRH1 | |
| Cytomap | 11q12.1 | |
| Gene Type | protein-coding | GO ID | GO:0006950 | UniProtAcc | Q86UN3 |
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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 |
| 349667 | RTN4RL2 | HCC1_Meng | Human | Liver | HCC | 8.77e-39 | 1.08e-01 | 0.0246 |
| 349667 | RTN4RL2 | HCC1 | Human | Liver | HCC | 3.04e-04 | 1.45e+00 | 0.5336 |
| 349667 | RTN4RL2 | HCC2 | Human | Liver | HCC | 1.03e-17 | 2.90e+00 | 0.5341 |
| 349667 | RTN4RL2 | S014 | Human | Liver | HCC | 1.04e-02 | 2.32e-01 | 0.2254 |
| 349667 | RTN4RL2 | S015 | Human | Liver | HCC | 8.79e-07 | 3.94e-01 | 0.2375 |
| 349667 | RTN4RL2 | S016 | Human | Liver | HCC | 5.68e-08 | 3.23e-01 | 0.2243 |
| 349667 | RTN4RL2 | S028 | Human | Liver | HCC | 1.46e-02 | 2.25e-01 | 0.2503 |
| 349667 | RTN4RL2 | S029 | Human | Liver | HCC | 2.86e-04 | 2.31e-01 | 0.2581 |
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| 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. |
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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:00310992 | Liver | HCC | regeneration | 107/7958 | 198/18723 | 6.67e-04 | 4.12e-03 | 107 |
| GO:001097511 | Liver | HCC | regulation of neuron projection development | 220/7958 | 445/18723 | 1.68e-03 | 8.78e-03 | 220 |
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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 |
| RTN4RL2 | SNV | Missense_Mutation | c.283T>A | p.Ser95Thr | p.S95T | Q86UN3 | protein_coding | tolerated(0.59) | benign(0.103) | TCGA-A8-A08Z-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RTN4RL2 | insertion | Frame_Shift_Ins | novel | c.206_207insCCTCCCGGGTT | p.Asn70LeufsTer116 | p.N70Lfs*116 | Q86UN3 | protein_coding | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RTN4RL2 | insertion | Frame_Shift_Ins | novel | c.208_209insC | p.Asn70ThrfsTer46 | p.N70Tfs*46 | Q86UN3 | protein_coding | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RTN4RL2 | SNV | Missense_Mutation | c.418C>T | p.Arg140Cys | p.R140C | Q86UN3 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-EK-A2PI-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| RTN4RL2 | SNV | Missense_Mutation | rs537129988 | c.218N>A | p.Arg73His | p.R73H | Q86UN3 | protein_coding | tolerated(0.14) | possibly_damaging(0.595) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RTN4RL2 | SNV | Missense_Mutation | rs140089941 | c.37N>A | p.Ala13Thr | p.A13T | Q86UN3 | protein_coding | tolerated_low_confidence(0.08) | benign(0.223) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
| RTN4RL2 | SNV | Missense_Mutation | rs755532417 | c.226C>T | p.Arg76Trp | p.R76W | Q86UN3 | protein_coding | deleterious(0.01) | probably_damaging(0.986) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| RTN4RL2 | SNV | Missense_Mutation | novel | c.713N>A | p.Ser238Asn | p.S238N | Q86UN3 | protein_coding | tolerated(0.55) | benign(0.031) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RTN4RL2 | SNV | Missense_Mutation | novel | c.212N>A | p.Leu71His | p.L71H | Q86UN3 | protein_coding | tolerated(0.19) | benign(0.036) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RTN4RL2 | SNV | Missense_Mutation | novel | c.431N>A | p.Ser144Asn | p.S144N | Q86UN3 | protein_coding | tolerated(0.11) | benign(0.022) | TCGA-AP-A1DK-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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