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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:00455983 | Oral cavity | OSCC | regulation of fat cell differentiation | 77/7305 | 139/18723 | 6.36e-05 | 5.18e-04 | 77 |
| GO:00072548 | Oral cavity | OSCC | JNK cascade | 90/7305 | 167/18723 | 6.49e-05 | 5.26e-04 | 90 |
| GO:00463288 | Oral cavity | OSCC | regulation of JNK cascade | 74/7305 | 133/18723 | 7.22e-05 | 5.69e-04 | 74 |
| GO:20010213 | Oral cavity | OSCC | negative regulation of response to DNA damage stimulus | 49/7305 | 81/18723 | 7.27e-05 | 5.72e-04 | 49 |
| GO:000164910 | Oral cavity | OSCC | osteoblast differentiation | 118/7305 | 229/18723 | 7.51e-05 | 5.85e-04 | 118 |
| GO:00140208 | Oral cavity | OSCC | primary neural tube formation | 55/7305 | 94/18723 | 9.87e-05 | 7.43e-04 | 55 |
| GO:001063118 | Oral cavity | OSCC | epithelial cell migration | 174/7305 | 357/18723 | 1.04e-04 | 7.70e-04 | 174 |
| GO:00018437 | Oral cavity | OSCC | neural tube closure | 52/7305 | 88/18723 | 1.06e-04 | 7.84e-04 | 52 |
| GO:006082810 | Oral cavity | OSCC | regulation of canonical Wnt signaling pathway | 128/7305 | 253/18723 | 1.11e-04 | 8.16e-04 | 128 |
| GO:009013218 | Oral cavity | OSCC | epithelium migration | 175/7305 | 360/18723 | 1.18e-04 | 8.54e-04 | 175 |
| GO:00456006 | Oral cavity | OSCC | positive regulation of fat cell differentiation | 41/7305 | 66/18723 | 1.20e-04 | 8.60e-04 | 41 |
| GO:19049504 | Oral cavity | OSCC | negative regulation of establishment of protein localization | 72/7305 | 131/18723 | 1.51e-04 | 1.06e-03 | 72 |
| GO:00606066 | Oral cavity | OSCC | tube closure | 52/7305 | 89/18723 | 1.59e-04 | 1.10e-03 | 52 |
| GO:00512243 | Oral cavity | OSCC | negative regulation of protein transport | 70/7305 | 127/18723 | 1.65e-04 | 1.14e-03 | 70 |
| GO:009013018 | Oral cavity | OSCC | tissue migration | 176/7305 | 365/18723 | 1.92e-04 | 1.29e-03 | 176 |
| GO:005134618 | Oral cavity | OSCC | negative regulation of hydrolase activity | 182/7305 | 379/18723 | 1.98e-04 | 1.32e-03 | 182 |
| GO:001097510 | Oral cavity | OSCC | regulation of neuron projection development | 210/7305 | 445/18723 | 2.35e-04 | 1.52e-03 | 210 |
| GO:001095117 | Oral cavity | OSCC | negative regulation of endopeptidase activity | 126/7305 | 252/18723 | 2.37e-04 | 1.54e-03 | 126 |
| GO:001046618 | Oral cavity | OSCC | negative regulation of peptidase activity | 130/7305 | 262/18723 | 2.89e-04 | 1.82e-03 | 130 |
| GO:006007010 | Oral cavity | OSCC | canonical Wnt signaling pathway | 148/7305 | 303/18723 | 2.89e-04 | 1.82e-03 | 148 |
| 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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