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Gene: RP2 |
Gene summary for RP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RP2 | Gene ID | 6102 |
| Gene name | RP2 activator of ARL3 GTPase | |
| Gene Alias | DELXp11.3 | |
| Cytomap | Xp11.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A0A1B2JLU2 |
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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 |
| 6102 | RP2 | HCC1_Meng | Human | Liver | HCC | 3.70e-16 | -1.45e-02 | 0.0246 |
| 6102 | RP2 | HCC2_Meng | Human | Liver | HCC | 2.51e-10 | 3.31e-02 | 0.0107 |
| 6102 | RP2 | HCC1 | Human | Liver | HCC | 8.75e-20 | 4.36e+00 | 0.5336 |
| 6102 | RP2 | S027 | Human | Liver | HCC | 4.76e-05 | 6.01e-01 | 0.2446 |
| 6102 | RP2 | S028 | Human | Liver | HCC | 3.73e-10 | 5.30e-01 | 0.2503 |
| 6102 | RP2 | S029 | Human | Liver | HCC | 1.76e-16 | 7.54e-01 | 0.2581 |
| 6102 | RP2 | male-WTA | Human | Thyroid | PTC | 4.35e-04 | -1.97e-02 | 0.1037 |
| 6102 | RP2 | PTC04 | Human | Thyroid | PTC | 1.81e-02 | 1.34e-02 | 0.1927 |
| 6102 | RP2 | PTC07 | Human | Thyroid | PTC | 1.52e-06 | 1.42e-02 | 0.2044 |
| 6102 | RP2 | ATC12 | Human | Thyroid | ATC | 2.64e-02 | -4.87e-03 | 0.34 |
| 6102 | RP2 | ATC13 | Human | Thyroid | ATC | 4.65e-23 | 9.51e-02 | 0.34 |
| 6102 | RP2 | ATC2 | Human | Thyroid | ATC | 5.54e-15 | 1.02e+00 | 0.34 |
| 6102 | RP2 | ATC5 | Human | Thyroid | ATC | 3.28e-12 | 1.14e-01 | 0.34 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:001063218 | Oral cavity | OSCC | regulation of epithelial cell migration | 136/7305 | 292/18723 | 4.82e-03 | 1.92e-02 | 136 |
| GO:00486759 | Oral cavity | OSCC | axon extension | 61/7305 | 120/18723 | 5.52e-03 | 2.14e-02 | 61 |
| GO:00171451 | Oral cavity | OSCC | stem cell division | 19/7305 | 30/18723 | 6.03e-03 | 2.28e-02 | 19 |
| GO:00147067 | Oral cavity | OSCC | striated muscle tissue development | 174/7305 | 384/18723 | 6.45e-03 | 2.40e-02 | 174 |
| GO:00605629 | Oral cavity | OSCC | epithelial tube morphogenesis | 149/7305 | 325/18723 | 6.73e-03 | 2.50e-02 | 149 |
| GO:0033138 | Oral cavity | OSCC | positive regulation of peptidyl-serine phosphorylation | 55/7305 | 108/18723 | 7.75e-03 | 2.84e-02 | 55 |
| GO:00434107 | Oral cavity | OSCC | positive regulation of MAPK cascade | 213/7305 | 480/18723 | 8.71e-03 | 3.16e-02 | 213 |
| GO:00435062 | Oral cavity | OSCC | regulation of JUN kinase activity | 32/7305 | 58/18723 | 9.08e-03 | 3.26e-02 | 32 |
| GO:003103217 | Oral cavity | OSCC | actomyosin structure organization | 93/7305 | 196/18723 | 9.63e-03 | 3.41e-02 | 93 |
| GO:006156410 | Oral cavity | OSCC | axon development | 207/7305 | 467/18723 | 1.01e-02 | 3.51e-02 | 207 |
| GO:00456674 | Oral cavity | OSCC | regulation of osteoblast differentiation | 65/7305 | 132/18723 | 1.06e-02 | 3.60e-02 | 65 |
| GO:003090116 | Oral cavity | OSCC | midbrain development | 46/7305 | 90/18723 | 1.30e-02 | 4.33e-02 | 46 |
| GO:00487627 | Oral cavity | OSCC | mesenchymal cell differentiation | 109/7305 | 236/18723 | 1.43e-02 | 4.69e-02 | 109 |
| GO:00488637 | Oral cavity | OSCC | stem cell differentiation | 96/7305 | 206/18723 | 1.55e-02 | 4.99e-02 | 96 |
| GO:000645719 | Oral cavity | LP | protein folding | 125/4623 | 212/18723 | 1.62e-26 | 8.45e-24 | 125 |
| GO:0097193110 | Oral cavity | LP | intrinsic apoptotic signaling pathway | 146/4623 | 288/18723 | 9.76e-22 | 2.78e-19 | 146 |
| GO:0034976110 | Oral cavity | LP | response to endoplasmic reticulum stress | 133/4623 | 256/18723 | 3.84e-21 | 9.24e-19 | 133 |
| GO:2001233110 | Oral cavity | LP | regulation of apoptotic signaling pathway | 168/4623 | 356/18723 | 1.35e-20 | 3.02e-18 | 168 |
| GO:2001242110 | Oral cavity | LP | regulation of intrinsic apoptotic signaling pathway | 95/4623 | 164/18723 | 9.85e-20 | 1.99e-17 | 95 |
| GO:0045862110 | Oral cavity | LP | positive regulation of proteolysis | 165/4623 | 372/18723 | 5.40e-17 | 8.46e-15 | 165 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 |
| 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 |
| SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | Breast | ADJ |
| SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Breast | DCIS |
| SEMA3C | NRP2_PLXNA2 | SEMA3C_NRP2_PLXNA2 | SEMA3 | Breast | Healthy |
| SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | Breast | Healthy |
| SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Breast | Healthy |
| SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Cervix | ADJ |
| SEMA3C | NRP2_PLXNA2 | SEMA3C_NRP2_PLXNA2 | SEMA3 | Cervix | CC |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | Cervix | CC |
| SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Cervix | CC |
| SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | Cervix | Precancer |
| SEMA3C | NRP2_PLXNA2 | SEMA3C_NRP2_PLXNA2 | SEMA3 | CRC | AD |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | CRC | AD |
| SEMA3C | NRP1_NRP2 | SEMA3C_NRP1_NRP2 | SEMA3 | CRC | AD |
| SEMA3B | NRP2_PLXNA2 | SEMA3B_NRP2_PLXNA2 | SEMA3 | CRC | ADJ |
| SEMA3C | NRP2_PLXNA2 | SEMA3C_NRP2_PLXNA2 | SEMA3 | CRC | ADJ |
| SEMA3B | NRP2_PLXNA2 | SEMA3B_NRP2_PLXNA2 | SEMA3 | CRC | FAP |
| SEMA3C | NRP2_PLXNA2 | SEMA3C_NRP2_PLXNA2 | SEMA3 | CRC | FAP |
| SEMA3B | NRP2_PLXNA2 | SEMA3B_NRP2_PLXNA2 | SEMA3 | CRC | MSI-H |
| SEMA3C | NRP2_PLXNA2 | SEMA3C_NRP2_PLXNA2 | SEMA3 | CRC | MSI-H |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | CRC | MSI-H |
| 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 |
| RP2 | SNV | Missense_Mutation | c.44C>G | p.Ser15Trp | p.S15W | O75695 | protein_coding | deleterious(0.01) | benign(0.176) | TCGA-BH-A208-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RP2 | SNV | Missense_Mutation | c.884G>A | p.Gly295Asp | p.G295D | O75695 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-GM-A2DK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | CR | |
| RP2 | SNV | Missense_Mutation | c.874C>A | p.Leu292Met | p.L292M | O75695 | protein_coding | deleterious(0.05) | possibly_damaging(0.468) | TCGA-UC-A7PF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RP2 | SNV | Missense_Mutation | novel | c.176N>A | p.Gly59Glu | p.G59E | O75695 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RP2 | SNV | Missense_Mutation | c.301N>C | p.Phe101Leu | p.F101L | O75695 | protein_coding | deleterious(0) | possibly_damaging(0.893) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| RP2 | SNV | Missense_Mutation | c.628G>A | p.Val210Ile | p.V210I | O75695 | protein_coding | tolerated(0.24) | benign(0) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RP2 | SNV | Missense_Mutation | c.467N>A | p.Ala156Asp | p.A156D | O75695 | protein_coding | tolerated(0.44) | benign(0.045) | TCGA-AG-4015-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RP2 | SNV | Missense_Mutation | novel | c.521N>C | p.Ile174Thr | p.I174T | O75695 | protein_coding | deleterious(0) | possibly_damaging(0.889) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| RP2 | SNV | Missense_Mutation | novel | c.721T>G | p.Phe241Val | p.F241V | O75695 | protein_coding | deleterious(0) | possibly_damaging(0.854) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RP2 | SNV | Missense_Mutation | novel | c.536N>A | p.Pro179His | p.P179H | O75695 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-AJ-A3BH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | 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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