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Gene: RCHY1 |
Gene summary for RCHY1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RCHY1 | Gene ID | 25898 |
| Gene name | ring finger and CHY zinc finger domain containing 1 | |
| Gene Alias | ARNIP | |
| Cytomap | 4q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000731 | UniProtAcc | Q96PM5 |
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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 |
| 25898 | RCHY1 | LZE3D | Human | Esophagus | HGIN | 4.81e-03 | 5.15e-01 | 0.0668 |
| 25898 | RCHY1 | LZE4T | Human | Esophagus | ESCC | 3.35e-09 | 2.84e-01 | 0.0811 |
| 25898 | RCHY1 | LZE7T | Human | Esophagus | ESCC | 5.11e-08 | 4.36e-01 | 0.0667 |
| 25898 | RCHY1 | LZE8T | Human | Esophagus | ESCC | 1.43e-05 | 2.06e-01 | 0.067 |
| 25898 | RCHY1 | LZE22T | Human | Esophagus | ESCC | 2.50e-03 | 2.38e-01 | 0.068 |
| 25898 | RCHY1 | LZE24T | Human | Esophagus | ESCC | 1.31e-06 | 1.42e-01 | 0.0596 |
| 25898 | RCHY1 | LZE6T | Human | Esophagus | ESCC | 1.81e-10 | 2.70e-01 | 0.0845 |
| 25898 | RCHY1 | P1T-E | Human | Esophagus | ESCC | 4.56e-03 | 2.26e-01 | 0.0875 |
| 25898 | RCHY1 | P2T-E | Human | Esophagus | ESCC | 9.04e-36 | 6.12e-01 | 0.1177 |
| 25898 | RCHY1 | P4T-E | Human | Esophagus | ESCC | 6.28e-29 | 5.74e-01 | 0.1323 |
| 25898 | RCHY1 | P5T-E | Human | Esophagus | ESCC | 1.34e-08 | 1.58e-01 | 0.1327 |
| 25898 | RCHY1 | P8T-E | Human | Esophagus | ESCC | 3.47e-18 | 2.51e-01 | 0.0889 |
| 25898 | RCHY1 | P9T-E | Human | Esophagus | ESCC | 2.31e-05 | 9.26e-02 | 0.1131 |
| 25898 | RCHY1 | P10T-E | Human | Esophagus | ESCC | 5.59e-17 | 3.05e-01 | 0.116 |
| 25898 | RCHY1 | P11T-E | Human | Esophagus | ESCC | 6.72e-13 | 4.08e-01 | 0.1426 |
| 25898 | RCHY1 | P12T-E | Human | Esophagus | ESCC | 4.63e-18 | 3.12e-01 | 0.1122 |
| 25898 | RCHY1 | P15T-E | Human | Esophagus | ESCC | 2.00e-21 | 4.65e-01 | 0.1149 |
| 25898 | RCHY1 | P16T-E | Human | Esophagus | ESCC | 2.60e-20 | 4.52e-01 | 0.1153 |
| 25898 | RCHY1 | P17T-E | Human | Esophagus | ESCC | 1.88e-02 | 1.53e-01 | 0.1278 |
| 25898 | RCHY1 | P20T-E | Human | Esophagus | ESCC | 6.31e-08 | 9.54e-02 | 0.1124 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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. |
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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:190332216 | Esophagus | ESCC | positive regulation of protein modification by small protein conjugation or removal | 99/8552 | 138/18723 | 4.39e-10 | 1.16e-08 | 99 |
| GO:003139816 | Esophagus | ESCC | positive regulation of protein ubiquitination | 82/8552 | 119/18723 | 2.41e-07 | 3.64e-06 | 82 |
| GO:00063012 | Esophagus | ESCC | postreplication repair | 26/8552 | 31/18723 | 1.32e-05 | 1.21e-04 | 26 |
| GO:0019985 | Esophagus | ESCC | translesion synthesis | 17/8552 | 21/18723 | 1.03e-03 | 5.19e-03 | 17 |
| GO:001049812 | Liver | Cirrhotic | proteasomal protein catabolic process | 216/4634 | 490/18723 | 2.52e-21 | 9.29e-19 | 216 |
| GO:004217612 | Liver | Cirrhotic | regulation of protein catabolic process | 181/4634 | 391/18723 | 7.94e-21 | 2.77e-18 | 181 |
| GO:000989612 | Liver | Cirrhotic | positive regulation of catabolic process | 215/4634 | 492/18723 | 1.13e-20 | 3.56e-18 | 215 |
| GO:003133112 | Liver | Cirrhotic | positive regulation of cellular catabolic process | 190/4634 | 427/18723 | 1.94e-19 | 4.18e-17 | 190 |
| GO:004316112 | Liver | Cirrhotic | proteasome-mediated ubiquitin-dependent protein catabolic process | 184/4634 | 412/18723 | 4.52e-19 | 8.85e-17 | 184 |
| GO:190336212 | Liver | Cirrhotic | regulation of cellular protein catabolic process | 124/4634 | 255/18723 | 9.85e-17 | 1.26e-14 | 124 |
| GO:004586212 | Liver | Cirrhotic | positive regulation of proteolysis | 163/4634 | 372/18723 | 4.18e-16 | 5.14e-14 | 163 |
| GO:004573212 | Liver | Cirrhotic | positive regulation of protein catabolic process | 112/4634 | 231/18723 | 3.89e-15 | 4.21e-13 | 112 |
| GO:190336412 | Liver | Cirrhotic | positive regulation of cellular protein catabolic process | 80/4634 | 155/18723 | 5.04e-13 | 3.86e-11 | 80 |
| GO:190305012 | Liver | Cirrhotic | regulation of proteolysis involved in cellular protein catabolic process | 103/4634 | 221/18723 | 1.14e-12 | 8.61e-11 | 103 |
| GO:200005812 | Liver | Cirrhotic | regulation of ubiquitin-dependent protein catabolic process | 81/4634 | 164/18723 | 7.22e-12 | 4.92e-10 | 81 |
| GO:190332012 | Liver | Cirrhotic | regulation of protein modification by small protein conjugation or removal | 105/4634 | 242/18723 | 1.43e-10 | 7.43e-09 | 105 |
| GO:006113612 | Liver | Cirrhotic | regulation of proteasomal protein catabolic process | 84/4634 | 187/18723 | 1.28e-09 | 5.56e-08 | 84 |
| GO:190305211 | Liver | Cirrhotic | positive regulation of proteolysis involved in cellular protein catabolic process | 64/4634 | 133/18723 | 4.23e-09 | 1.70e-07 | 64 |
| GO:003243412 | Liver | Cirrhotic | regulation of proteasomal ubiquitin-dependent protein catabolic process | 64/4634 | 134/18723 | 6.16e-09 | 2.40e-07 | 64 |
| GO:003139612 | Liver | Cirrhotic | regulation of protein ubiquitination | 89/4634 | 210/18723 | 1.40e-08 | 5.30e-07 | 89 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0412027 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa0411524 | Esophagus | ESCC | p53 signaling pathway | 65/4205 | 74/8465 | 3.88e-12 | 6.50e-11 | 3.33e-11 | 65 |
| hsa051629 | Esophagus | ESCC | Measles | 90/4205 | 139/8465 | 2.16e-04 | 7.87e-04 | 4.03e-04 | 90 |
| hsa0412036 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa0411534 | Esophagus | ESCC | p53 signaling pathway | 65/4205 | 74/8465 | 3.88e-12 | 6.50e-11 | 3.33e-11 | 65 |
| hsa0516213 | Esophagus | ESCC | Measles | 90/4205 | 139/8465 | 2.16e-04 | 7.87e-04 | 4.03e-04 | 90 |
| hsa0412021 | Liver | Cirrhotic | Ubiquitin mediated proteolysis | 72/2530 | 142/8465 | 1.32e-07 | 1.97e-06 | 1.21e-06 | 72 |
| hsa0412031 | Liver | Cirrhotic | Ubiquitin mediated proteolysis | 72/2530 | 142/8465 | 1.32e-07 | 1.97e-06 | 1.21e-06 | 72 |
| hsa0412041 | Liver | HCC | Ubiquitin mediated proteolysis | 110/4020 | 142/8465 | 1.67e-13 | 3.74e-12 | 2.08e-12 | 110 |
| hsa041156 | Liver | HCC | p53 signaling pathway | 46/4020 | 74/8465 | 7.64e-03 | 2.08e-02 | 1.16e-02 | 46 |
| hsa0412051 | Liver | HCC | Ubiquitin mediated proteolysis | 110/4020 | 142/8465 | 1.67e-13 | 3.74e-12 | 2.08e-12 | 110 |
| hsa0411511 | Liver | HCC | p53 signaling pathway | 46/4020 | 74/8465 | 7.64e-03 | 2.08e-02 | 1.16e-02 | 46 |
| 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 |
| 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 |
| RCHY1 | SNV | Missense_Mutation | c.640N>G | p.Gln214Glu | p.Q214E | Q96PM5 | protein_coding | tolerated(0.41) | benign(0.031) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| RCHY1 | SNV | Missense_Mutation | rs766486122 | c.53G>A | p.Arg18Gln | p.R18Q | Q96PM5 | protein_coding | tolerated(0.24) | benign(0) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RCHY1 | SNV | Missense_Mutation | c.37C>G | p.Gln13Glu | p.Q13E | Q96PM5 | protein_coding | tolerated(1) | benign(0) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RCHY1 | insertion | Nonsense_Mutation | novel | c.677_678insGAGACAACAGTGAACAATAAAGATAAAAGTCCTTGTCCTCAC | p.Asn226delinsLysArgGlnGlnTerThrIleLysIleLysValLeuValLeuThr | p.N226delinsKRQQ*TIKIKVLVLT | Q96PM5 | protein_coding | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RCHY1 | SNV | Missense_Mutation | c.44N>A | p.Arg15Gln | p.R15Q | Q96PM5 | protein_coding | tolerated(0.5) | benign(0) | TCGA-C5-A1BI-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| RCHY1 | SNV | Missense_Mutation | novel | c.528N>A | p.Met176Ile | p.M176I | Q96PM5 | protein_coding | deleterious(0.01) | benign(0.012) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RCHY1 | SNV | Missense_Mutation | novel | c.520N>A | p.Glu174Lys | p.E174K | Q96PM5 | protein_coding | tolerated(0.42) | benign(0.046) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| RCHY1 | SNV | Missense_Mutation | novel | c.219G>C | p.Gln73His | p.Q73H | Q96PM5 | protein_coding | deleterious(0.01) | possibly_damaging(0.809) | TCGA-ZJ-AB0I-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RCHY1 | deletion | Frame_Shift_Del | c.202delA | p.Ile68PhefsTer53 | p.I68Ffs*53 | Q96PM5 | protein_coding | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | |||
| RCHY1 | SNV | Missense_Mutation | c.545N>A | p.Arg182Lys | p.R182K | Q96PM5 | protein_coding | tolerated(0.09) | benign(0.381) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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