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Gene: RETREG1 |
Gene summary for RETREG1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RETREG1 | Gene ID | 54463 |
| Gene name | reticulophagy regulator 1 | |
| Gene Alias | FAM134B | |
| Cytomap | 5p15.1 | |
| Gene Type | protein-coding | GO ID | GO:0000422 | UniProtAcc | Q9H6L5 |
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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 |
| 54463 | RETREG1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.68e-05 | 4.76e-01 | -0.0811 |
| 54463 | RETREG1 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.82e-16 | 6.97e-01 | -0.1954 |
| 54463 | RETREG1 | HTA11_411_2000001011 | Human | Colorectum | SER | 7.14e-08 | 1.24e+00 | -0.2602 |
| 54463 | RETREG1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.79e-06 | 1.02e+00 | -0.2196 |
| 54463 | RETREG1 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.44e-05 | 4.14e-01 | -0.1001 |
| 54463 | RETREG1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.91e-02 | 5.74e-01 | -0.2061 |
| 54463 | RETREG1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.23e-23 | -4.77e-01 | 0.294 |
| 54463 | RETREG1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.60e-07 | -4.77e-01 | 0.281 |
| 54463 | RETREG1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.18e-24 | -4.77e-01 | 0.3859 |
| 54463 | RETREG1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.82e-05 | -4.77e-01 | 0.2585 |
| 54463 | RETREG1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.84e-22 | -4.77e-01 | 0.3005 |
| 54463 | RETREG1 | A015-C-203 | Human | Colorectum | FAP | 1.04e-08 | 7.72e-02 | -0.1294 |
| 54463 | RETREG1 | A002-C-201 | Human | Colorectum | FAP | 1.27e-03 | -1.39e-01 | 0.0324 |
| 54463 | RETREG1 | A001-C-119 | Human | Colorectum | FAP | 3.91e-02 | 1.41e-01 | -0.1557 |
| 54463 | RETREG1 | A001-C-108 | Human | Colorectum | FAP | 2.59e-03 | 1.19e-01 | -0.0272 |
| 54463 | RETREG1 | A002-C-205 | Human | Colorectum | FAP | 5.42e-09 | -1.71e-01 | -0.1236 |
| 54463 | RETREG1 | A015-C-005 | Human | Colorectum | FAP | 3.81e-06 | 4.58e-01 | -0.0336 |
| 54463 | RETREG1 | A015-C-006 | Human | Colorectum | FAP | 9.88e-04 | -2.06e-01 | -0.0994 |
| 54463 | RETREG1 | A002-C-114 | Human | Colorectum | FAP | 2.72e-06 | -3.75e-02 | -0.1561 |
| 54463 | RETREG1 | A015-C-104 | Human | Colorectum | FAP | 1.59e-11 | -2.38e-02 | -0.1899 |
| Page: 1 2 3 |
| 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 | ||
| 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:0022411 | Colorectum | AD | cellular component disassembly | 147/3918 | 443/18723 | 8.53e-10 | 6.76e-08 | 147 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0070997 | Colorectum | AD | neuron death | 114/3918 | 361/18723 | 1.13e-06 | 3.72e-05 | 114 |
| GO:1903008 | Colorectum | AD | organelle disassembly | 46/3918 | 114/18723 | 1.81e-06 | 5.48e-05 | 46 |
| GO:0000422 | Colorectum | AD | autophagy of mitochondrion | 35/3918 | 81/18723 | 4.94e-06 | 1.29e-04 | 35 |
| GO:0061726 | Colorectum | AD | mitochondrion disassembly | 35/3918 | 81/18723 | 4.94e-06 | 1.29e-04 | 35 |
| GO:1901214 | Colorectum | AD | regulation of neuron death | 99/3918 | 319/18723 | 1.26e-05 | 2.76e-04 | 99 |
| GO:0061912 | Colorectum | AD | selective autophagy | 29/3918 | 68/18723 | 4.20e-05 | 7.39e-04 | 29 |
| GO:0051402 | Colorectum | AD | neuron apoptotic process | 77/3918 | 246/18723 | 8.07e-05 | 1.28e-03 | 77 |
| GO:1901215 | Colorectum | AD | negative regulation of neuron death | 67/3918 | 208/18723 | 8.81e-05 | 1.35e-03 | 67 |
| GO:0000423 | Colorectum | AD | mitophagy | 14/3918 | 28/18723 | 6.01e-04 | 6.33e-03 | 14 |
| GO:0043523 | Colorectum | AD | regulation of neuron apoptotic process | 64/3918 | 212/18723 | 8.95e-04 | 8.63e-03 | 64 |
| GO:0043524 | Colorectum | AD | negative regulation of neuron apoptotic process | 43/3918 | 145/18723 | 8.04e-03 | 4.73e-02 | 43 |
| GO:00224111 | Colorectum | SER | cellular component disassembly | 114/2897 | 443/18723 | 1.17e-08 | 9.59e-07 | 114 |
| GO:00162361 | Colorectum | SER | macroautophagy | 79/2897 | 291/18723 | 1.97e-07 | 1.10e-05 | 79 |
| GO:00004221 | Colorectum | SER | autophagy of mitochondrion | 29/2897 | 81/18723 | 5.61e-06 | 2.01e-04 | 29 |
| GO:00617261 | Colorectum | SER | mitochondrion disassembly | 29/2897 | 81/18723 | 5.61e-06 | 2.01e-04 | 29 |
| GO:19030081 | Colorectum | SER | organelle disassembly | 36/2897 | 114/18723 | 1.22e-05 | 3.89e-04 | 36 |
| GO:00619121 | Colorectum | SER | selective autophagy | 24/2897 | 68/18723 | 4.60e-05 | 1.15e-03 | 24 |
| GO:00709971 | Colorectum | SER | neuron death | 84/2897 | 361/18723 | 5.76e-05 | 1.35e-03 | 84 |
| Page: 1 2 3 4 5 |
| 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 |
| Page: 1 |
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