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Gene: RGPD5 |
Gene summary for RGPD5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RGPD5 | Gene ID | 84220 |
| Gene name | RANBP2 like and GRIP domain containing 5 | |
| Gene Alias | BS-63 | |
| Cytomap | 2q13 | |
| Gene Type | protein-coding | GO ID | GO:0006606 | UniProtAcc | Q99666 |
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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 |
| 84220 | RGPD5 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.55e-09 | 1.88e-01 | 0.0155 |
| 84220 | RGPD5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 4.68e-08 | 2.32e-01 | -0.1808 |
| 84220 | RGPD5 | HTA11_2951_2000001011 | Human | Colorectum | AD | 2.79e-07 | 4.41e-01 | 0.0216 |
| 84220 | RGPD5 | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.84e-10 | 3.09e-01 | -0.0811 |
| 84220 | RGPD5 | HTA11_78_2000001011 | Human | Colorectum | AD | 6.85e-15 | 3.79e-01 | -0.1088 |
| 84220 | RGPD5 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.18e-22 | 4.19e-01 | -0.1954 |
| 84220 | RGPD5 | HTA11_411_2000001011 | Human | Colorectum | SER | 4.01e-04 | 3.68e-01 | -0.2602 |
| 84220 | RGPD5 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.71e-03 | 3.07e-01 | -0.2196 |
| 84220 | RGPD5 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.57e-07 | 2.24e-01 | -0.1207 |
| 84220 | RGPD5 | HTA11_83_2000001011 | Human | Colorectum | SER | 7.35e-06 | 2.31e-01 | -0.1526 |
| 84220 | RGPD5 | HTA11_696_2000001011 | Human | Colorectum | AD | 9.02e-22 | 3.78e-01 | -0.1464 |
| 84220 | RGPD5 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.02e-18 | 3.30e-01 | -0.1001 |
| 84220 | RGPD5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.99e-16 | 3.55e-01 | -0.059 |
| 84220 | RGPD5 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.72e-05 | 2.87e-01 | -0.1706 |
| 84220 | RGPD5 | HTA11_5216_2000001011 | Human | Colorectum | SER | 3.34e-04 | 2.52e-01 | -0.1462 |
| 84220 | RGPD5 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.56e-06 | 2.30e-01 | -0.0842 |
| 84220 | RGPD5 | HTA11_866_3004761011 | Human | Colorectum | AD | 5.92e-06 | 1.77e-01 | 0.096 |
| 84220 | RGPD5 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.40e-02 | 1.93e-01 | 0.0446 |
| 84220 | RGPD5 | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.19e-02 | 1.62e-01 | 0.0528 |
| 84220 | RGPD5 | HTA11_10623_2000001011 | Human | Colorectum | AD | 8.98e-03 | 1.67e-01 | -0.0177 |
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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:00725941 | Colorectum | SER | establishment of protein localization to organelle | 111/2897 | 422/18723 | 4.98e-09 | 4.49e-07 | 111 |
| GO:00069131 | Colorectum | SER | nucleocytoplasmic transport | 77/2897 | 301/18723 | 3.39e-06 | 1.32e-04 | 77 |
| GO:00511691 | Colorectum | SER | nuclear transport | 77/2897 | 301/18723 | 3.39e-06 | 1.32e-04 | 77 |
| GO:00345041 | Colorectum | SER | protein localization to nucleus | 74/2897 | 290/18723 | 5.74e-06 | 2.05e-04 | 74 |
| GO:00170381 | Colorectum | SER | protein import | 49/2897 | 206/18723 | 1.12e-03 | 1.29e-02 | 49 |
| GO:00511701 | Colorectum | SER | import into nucleus | 38/2897 | 159/18723 | 3.48e-03 | 2.95e-02 | 38 |
| GO:00066061 | Colorectum | SER | protein import into nucleus | 36/2897 | 155/18723 | 7.07e-03 | 4.98e-02 | 36 |
| 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 |
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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 |
| 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 |
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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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