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Gene: RGPD2 |
Gene summary for RGPD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RGPD2 | Gene ID | 729857 |
| Gene name | RANBP2 like and GRIP domain containing 2 | |
| Gene Alias | NUP358 | |
| Cytomap | 2p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0006606 | UniProtAcc | B4DYH0 |
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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 |
| 729857 | RGPD2 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.82e-07 | 2.78e-01 | -0.1954 |
| 729857 | RGPD2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.98e-19 | 4.48e-01 | -0.1464 |
| 729857 | RGPD2 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.01e-03 | 2.03e-01 | -0.1001 |
| 729857 | RGPD2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 4.07e-02 | 5.59e-01 | 0.3487 |
| 729857 | RGPD2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.01e-48 | 1.31e+00 | 0.281 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0006913 | Colorectum | AD | nucleocytoplasmic transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0051169 | Colorectum | AD | nuclear transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0034504 | Colorectum | AD | protein localization to nucleus | 94/3918 | 290/18723 | 2.83e-06 | 8.09e-05 | 94 |
| GO:0017038 | Colorectum | AD | protein import | 67/3918 | 206/18723 | 6.34e-05 | 1.05e-03 | 67 |
| GO:0051170 | Colorectum | AD | import into nucleus | 53/3918 | 159/18723 | 1.76e-04 | 2.38e-03 | 53 |
| GO:0006606 | Colorectum | AD | protein import into nucleus | 51/3918 | 155/18723 | 3.29e-04 | 3.86e-03 | 51 |
| GO:00725942 | Colorectum | MSS | establishment of protein localization to organelle | 139/3467 | 422/18723 | 5.75e-13 | 1.12e-10 | 139 |
| GO:00069132 | Colorectum | MSS | nucleocytoplasmic transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
| GO:00511692 | Colorectum | MSS | nuclear transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
| GO:00345042 | Colorectum | MSS | protein localization to nucleus | 92/3467 | 290/18723 | 3.66e-08 | 1.98e-06 | 92 |
| GO:00170382 | Colorectum | MSS | protein import | 65/3467 | 206/18723 | 4.28e-06 | 1.22e-04 | 65 |
| GO:00511702 | Colorectum | MSS | import into nucleus | 52/3467 | 159/18723 | 1.23e-05 | 2.87e-04 | 52 |
| GO:00066062 | Colorectum | MSS | protein import into nucleus | 50/3467 | 155/18723 | 2.72e-05 | 5.58e-04 | 50 |
| GO:0006607 | Colorectum | MSS | NLS-bearing protein import into nucleus | 10/3467 | 20/18723 | 1.40e-03 | 1.32e-02 | 10 |
| GO:00725943 | Colorectum | MSI-H | establishment of protein localization to organelle | 63/1319 | 422/18723 | 1.10e-08 | 1.33e-06 | 63 |
| GO:00069133 | Colorectum | MSI-H | nucleocytoplasmic transport | 45/1319 | 301/18723 | 1.31e-06 | 8.75e-05 | 45 |
| GO:00511693 | Colorectum | MSI-H | nuclear transport | 45/1319 | 301/18723 | 1.31e-06 | 8.75e-05 | 45 |
| GO:00345043 | Colorectum | MSI-H | protein localization to nucleus | 40/1319 | 290/18723 | 3.43e-05 | 1.33e-03 | 40 |
| GO:00170383 | Colorectum | MSI-H | protein import | 29/1319 | 206/18723 | 2.76e-04 | 6.90e-03 | 29 |
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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 |
| RGPD2 | SNV | Missense_Mutation | novel | c.4125N>T | p.Lys1375Asn | p.K1375N | P0DJD1 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A8-A08F-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| RGPD2 | SNV | Missense_Mutation | novel | c.2644C>G | p.Leu882Val | p.L882V | P0DJD1 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AN-A0AR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RGPD2 | SNV | Missense_Mutation | novel | c.78N>C | p.Leu26Phe | p.L26F | P0DJD1 | protein_coding | deleterious(0.01) | benign(0.001) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| RGPD2 | SNV | Missense_Mutation | novel | c.3982N>C | p.Glu1328Gln | p.E1328Q | P0DJD1 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RGPD2 | SNV | Missense_Mutation | c.5167N>T | p.Leu1723Phe | p.L1723F | P0DJD1 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.991) | TCGA-MY-A5BD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RGPD2 | SNV | Missense_Mutation | c.29N>A | p.Arg10Gln | p.R10Q | P0DJD1 | protein_coding | deleterious(0.01) | possibly_damaging(0.776) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RGPD2 | SNV | Missense_Mutation | novel | c.4420N>C | p.Ser1474Arg | p.S1474R | P0DJD1 | protein_coding | deleterious(0.03) | benign(0.138) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| RGPD2 | SNV | Missense_Mutation | c.8G>A | p.Arg3His | p.R3H | P0DJD1 | protein_coding | deleterious(0) | probably_damaging(0.923) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RGPD2 | SNV | Missense_Mutation | c.55N>A | p.Ala19Thr | p.A19T | P0DJD1 | protein_coding | tolerated(0.2) | benign(0.034) | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RGPD2 | SNV | Missense_Mutation | novel | c.2781N>T | p.Lys927Asn | p.K927N | P0DJD1 | protein_coding | tolerated(0.16) | benign(0.051) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <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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