|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: RGN |
Gene summary for RGN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RGN | Gene ID | 9104 |
| Gene name | regucalcin | |
| Gene Alias | GNL | |
| Cytomap | Xp11.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q15493 |
Top |
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 |
| 9104 | RGN | NAFLD1 | Human | Liver | NAFLD | 5.11e-06 | 4.97e-01 | -0.04 |
| 9104 | RGN | S43 | Human | Liver | Cirrhotic | 4.66e-10 | -2.70e-01 | -0.0187 |
| 9104 | RGN | HCC1_Meng | Human | Liver | HCC | 3.12e-97 | -2.14e-02 | 0.0246 |
| 9104 | RGN | HCC2_Meng | Human | Liver | HCC | 1.47e-17 | -3.30e-01 | 0.0107 |
| 9104 | RGN | cirrhotic1 | Human | Liver | Cirrhotic | 4.21e-08 | -1.98e-01 | 0.0202 |
| 9104 | RGN | cirrhotic2 | Human | Liver | Cirrhotic | 1.45e-09 | -2.57e-01 | 0.0201 |
| 9104 | RGN | cirrhotic3 | Human | Liver | Cirrhotic | 2.19e-04 | -2.61e-01 | 0.0215 |
| 9104 | RGN | HCC1 | Human | Liver | HCC | 3.52e-41 | 6.20e+00 | 0.5336 |
| 9104 | RGN | Pt13.a | Human | Liver | HCC | 6.91e-04 | -9.02e-02 | 0.021 |
| 9104 | RGN | Pt13.b | Human | Liver | HCC | 4.21e-20 | -8.65e-02 | 0.0251 |
| 9104 | RGN | Pt14.b | Human | Liver | HCC | 3.11e-02 | -8.82e-02 | 0.018 |
| 9104 | RGN | Pt14.d | Human | Liver | HCC | 1.35e-05 | -2.27e-01 | 0.0143 |
| 9104 | RGN | S027 | Human | Liver | HCC | 8.43e-03 | 6.89e-01 | 0.2446 |
| 9104 | RGN | S028 | Human | Liver | HCC | 2.94e-13 | 8.63e-01 | 0.2503 |
| 9104 | RGN | S029 | Human | Liver | HCC | 4.14e-16 | 1.21e+00 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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. |
Top |
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:00160535 | Liver | NAFLD | organic acid biosynthetic process | 77/1882 | 316/18723 | 1.03e-13 | 6.69e-11 | 77 |
| GO:00463945 | Liver | NAFLD | carboxylic acid biosynthetic process | 75/1882 | 314/18723 | 6.37e-13 | 3.39e-10 | 75 |
| GO:00313317 | Liver | NAFLD | positive regulation of cellular catabolic process | 92/1882 | 427/18723 | 1.01e-12 | 4.91e-10 | 92 |
| GO:00442707 | Liver | NAFLD | cellular nitrogen compound catabolic process | 93/1882 | 451/18723 | 1.04e-11 | 4.34e-09 | 93 |
| GO:00467006 | Liver | NAFLD | heterocycle catabolic process | 92/1882 | 445/18723 | 1.16e-11 | 4.52e-09 | 92 |
| GO:00421767 | Liver | NAFLD | regulation of protein catabolic process | 83/1882 | 391/18723 | 2.94e-11 | 1.01e-08 | 83 |
| GO:19030507 | Liver | NAFLD | regulation of proteolysis involved in cellular protein catabolic process | 53/1882 | 221/18723 | 1.32e-09 | 2.34e-07 | 53 |
| GO:00346556 | Liver | NAFLD | nucleobase-containing compound catabolic process | 80/1882 | 407/18723 | 3.07e-09 | 4.61e-07 | 80 |
| GO:19033627 | Liver | NAFLD | regulation of cellular protein catabolic process | 56/1882 | 255/18723 | 1.38e-08 | 1.71e-06 | 56 |
| GO:00098957 | Liver | NAFLD | negative regulation of catabolic process | 65/1882 | 320/18723 | 2.50e-08 | 2.71e-06 | 65 |
| GO:00610087 | Liver | NAFLD | hepaticobiliary system development | 38/1882 | 150/18723 | 5.94e-08 | 5.42e-06 | 38 |
| GO:00313307 | Liver | NAFLD | negative regulation of cellular catabolic process | 55/1882 | 262/18723 | 9.35e-08 | 7.59e-06 | 55 |
| GO:00066413 | Liver | NAFLD | triglyceride metabolic process | 29/1882 | 100/18723 | 9.51e-08 | 7.62e-06 | 29 |
| GO:00018897 | Liver | NAFLD | liver development | 37/1882 | 147/18723 | 1.06e-07 | 8.12e-06 | 37 |
| GO:00059965 | Liver | NAFLD | monosaccharide metabolic process | 53/1882 | 257/18723 | 2.89e-07 | 1.92e-05 | 53 |
| GO:00723303 | Liver | NAFLD | monocarboxylic acid biosynthetic process | 46/1882 | 214/18723 | 5.06e-07 | 3.07e-05 | 46 |
| GO:00620125 | Liver | NAFLD | regulation of small molecule metabolic process | 63/1882 | 334/18723 | 6.55e-07 | 3.79e-05 | 63 |
| GO:00193185 | Liver | NAFLD | hexose metabolic process | 49/1882 | 237/18723 | 7.41e-07 | 4.12e-05 | 49 |
| GO:00457327 | Liver | NAFLD | positive regulation of protein catabolic process | 48/1882 | 231/18723 | 8.22e-07 | 4.45e-05 | 48 |
| GO:00066392 | Liver | NAFLD | acylglycerol metabolic process | 32/1882 | 128/18723 | 8.82e-07 | 4.60e-05 | 32 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0120010 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa0120011 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa0120021 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
| hsa01240 | Liver | Cirrhotic | Biosynthesis of cofactors | 66/2530 | 153/8465 | 3.11e-04 | 1.99e-03 | 1.23e-03 | 66 |
| hsa00030 | Liver | Cirrhotic | Pentose phosphate pathway | 16/2530 | 30/8465 | 6.04e-03 | 2.12e-02 | 1.30e-02 | 16 |
| hsa0120031 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
| hsa012401 | Liver | Cirrhotic | Biosynthesis of cofactors | 66/2530 | 153/8465 | 3.11e-04 | 1.99e-03 | 1.23e-03 | 66 |
| hsa000301 | Liver | Cirrhotic | Pentose phosphate pathway | 16/2530 | 30/8465 | 6.04e-03 | 2.12e-02 | 1.30e-02 | 16 |
| hsa0120041 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa012402 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
| hsa000302 | Liver | HCC | Pentose phosphate pathway | 21/4020 | 30/8465 | 1.06e-02 | 2.71e-02 | 1.51e-02 | 21 |
| hsa0120051 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa012403 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
| hsa000303 | Liver | HCC | Pentose phosphate pathway | 21/4020 | 30/8465 | 1.06e-02 | 2.71e-02 | 1.51e-02 | 21 |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| RGN | SNV | Missense_Mutation | rs782503509 | c.893N>T | p.Ala298Val | p.A298V | Q15493 | protein_coding | tolerated(0.11) | benign(0.003) | TCGA-A7-A56D-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| RGN | SNV | Missense_Mutation | c.190N>T | p.Arg64Cys | p.R64C | Q15493 | protein_coding | tolerated(0.09) | probably_damaging(0.998) | TCGA-BH-A1F8-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| RGN | SNV | Missense_Mutation | novel | c.291N>C | p.Lys97Asn | p.K97N | Q15493 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-MA-AA3Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RGN | SNV | Missense_Mutation | c.50N>A | p.Gly17Asp | p.G17D | Q15493 | protein_coding | deleterious(0.05) | probably_damaging(1) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| RGN | SNV | Missense_Mutation | novel | c.507C>A | p.Asp169Glu | p.D169E | Q15493 | protein_coding | deleterious(0) | possibly_damaging(0.695) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RGN | SNV | Missense_Mutation | novel | c.212N>T | p.Ala71Val | p.A71V | Q15493 | protein_coding | tolerated(1) | benign(0) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| RGN | SNV | Missense_Mutation | novel | c.830A>G | p.Glu277Gly | p.E277G | Q15493 | protein_coding | tolerated(0.15) | benign(0.019) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RGN | SNV | Missense_Mutation | novel | c.674N>C | p.Ile225Thr | p.I225T | Q15493 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RGN | SNV | Missense_Mutation | novel | c.572N>A | p.Arg191Lys | p.R191K | Q15493 | protein_coding | tolerated(0.05) | possibly_damaging(0.634) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| RGN | SNV | Missense_Mutation | c.575N>A | p.Ser192Asn | p.S192N | Q15493 | protein_coding | tolerated(0.49) | benign(0.025) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| Page: 1 2 3 4 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |