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Gene: RTN2 |
Gene summary for RTN2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RTN2 | Gene ID | 6253 |
| Gene name | reticulon 2 | |
| Gene Alias | NSP2 | |
| Cytomap | 19q13.32 | |
| Gene Type | protein-coding | GO ID | GO:0006518 | UniProtAcc | A8K7F2 |
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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 |
| 6253 | RTN2 | HCC1_Meng | Human | Liver | HCC | 1.89e-53 | 1.09e-01 | 0.0246 |
| 6253 | RTN2 | HCC2_Meng | Human | Liver | HCC | 1.82e-07 | 4.09e-02 | 0.0107 |
| 6253 | RTN2 | Pt13.b | Human | Liver | HCC | 4.70e-02 | 7.67e-02 | 0.0251 |
| 6253 | RTN2 | Pt14.a | Human | Liver | HCC | 9.06e-06 | 2.72e-01 | 0.0169 |
| 6253 | RTN2 | S014 | Human | Liver | HCC | 2.01e-15 | 5.25e-01 | 0.2254 |
| 6253 | RTN2 | S015 | Human | Liver | HCC | 8.20e-21 | 8.04e-01 | 0.2375 |
| 6253 | RTN2 | S016 | Human | Liver | HCC | 2.02e-22 | 5.31e-01 | 0.2243 |
| 6253 | RTN2 | C21 | Human | Oral cavity | OSCC | 9.52e-03 | 1.34e-01 | 0.2678 |
| 6253 | RTN2 | C30 | Human | Oral cavity | OSCC | 6.79e-12 | 5.57e-01 | 0.3055 |
| 6253 | RTN2 | C38 | Human | Oral cavity | OSCC | 6.26e-03 | 3.49e-01 | 0.172 |
| 6253 | RTN2 | C46 | Human | Oral cavity | OSCC | 3.11e-04 | 1.32e-01 | 0.1673 |
| 6253 | RTN2 | LN46 | Human | Oral cavity | OSCC | 9.73e-04 | 2.13e-01 | 0.1666 |
| 6253 | RTN2 | SYSMH2 | Human | Oral cavity | OSCC | 2.80e-05 | 9.00e-02 | 0.2326 |
| 6253 | RTN2 | SYSMH5 | Human | Oral cavity | OSCC | 3.24e-02 | 1.50e-01 | 0.0647 |
| 6253 | RTN2 | SYSMH6 | Human | Oral cavity | OSCC | 4.57e-03 | 1.20e-01 | 0.1275 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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. |
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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:007180611 | Liver | HCC | protein transmembrane transport | 47/7958 | 59/18723 | 5.82e-09 | 1.51e-07 | 47 |
| GO:006500211 | Liver | HCC | intracellular protein transmembrane transport | 41/7958 | 51/18723 | 3.41e-08 | 7.61e-07 | 41 |
| GO:003424921 | Liver | HCC | negative regulation of cellular amide metabolic process | 144/7958 | 273/18723 | 3.80e-04 | 2.61e-03 | 144 |
| GO:0008643 | Liver | HCC | carbohydrate transport | 80/7958 | 152/18723 | 7.34e-03 | 2.92e-02 | 80 |
| GO:00718068 | Oral cavity | OSCC | protein transmembrane transport | 43/7305 | 59/18723 | 1.32e-07 | 2.22e-06 | 43 |
| GO:00650025 | Oral cavity | OSCC | intracellular protein transmembrane transport | 36/7305 | 51/18723 | 4.79e-06 | 5.47e-05 | 36 |
| GO:00429873 | Oral cavity | OSCC | amyloid precursor protein catabolic process | 40/7305 | 68/18723 | 7.28e-04 | 3.98e-03 | 40 |
| GO:00429823 | Oral cavity | OSCC | amyloid precursor protein metabolic process | 52/7305 | 95/18723 | 1.33e-03 | 6.62e-03 | 52 |
| GO:00342495 | Oral cavity | OSCC | negative regulation of cellular amide metabolic process | 130/7305 | 273/18723 | 2.20e-03 | 1.00e-02 | 130 |
| GO:00504353 | Oral cavity | OSCC | amyloid-beta metabolic process | 36/7305 | 67/18723 | 1.01e-02 | 3.51e-02 | 36 |
| GO:00342052 | Oral cavity | OSCC | amyloid-beta formation | 31/7305 | 57/18723 | 1.32e-02 | 4.38e-02 | 31 |
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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. |
| 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 |
| RTN2 | SNV | Missense_Mutation | novel | c.344N>G | p.Leu115Arg | p.L115R | O75298 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RTN2 | SNV | Missense_Mutation | rs570062973 | c.403N>T | p.Arg135Cys | p.R135C | O75298 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-AR-A254-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| RTN2 | SNV | Missense_Mutation | c.649N>A | p.Gly217Ser | p.G217S | O75298 | protein_coding | tolerated_low_confidence(0.51) | benign(0.001) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RTN2 | SNV | Missense_Mutation | c.1060A>G | p.Thr354Ala | p.T354A | O75298 | protein_coding | tolerated(0.24) | benign(0.022) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| RTN2 | SNV | Missense_Mutation | c.895N>A | p.Leu299Met | p.L299M | O75298 | protein_coding | tolerated_low_confidence(0.1) | benign(0.372) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RTN2 | SNV | Missense_Mutation | rs781700125 | c.250N>T | p.Arg84Cys | p.R84C | O75298 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.965) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RTN2 | SNV | Missense_Mutation | novel | c.694N>A | p.Glu232Lys | p.E232K | O75298 | protein_coding | deleterious_low_confidence(0.01) | benign(0.04) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| RTN2 | SNV | Missense_Mutation | c.628N>T | p.Gly210Cys | p.G210C | O75298 | protein_coding | tolerated_low_confidence(0.07) | possibly_damaging(0.533) | TCGA-DS-A0VK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
| RTN2 | SNV | Missense_Mutation | c.676N>A | p.Asp226Asn | p.D226N | O75298 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.616) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RTN2 | SNV | Missense_Mutation | novel | c.1438N>G | p.Leu480Val | p.L480V | O75298 | protein_coding | tolerated(0.08) | possibly_damaging(0.56) | TCGA-VS-A94W-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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