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Gene: YBEY |
Gene summary for YBEY |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YBEY | Gene ID | 54059 |
| Gene name | ybeY metalloendoribonuclease | |
| Gene Alias | C21orf57 | |
| Cytomap | 21q22.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q8TBC8 |
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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 |
| 54059 | YBEY | LZE7T | Human | Esophagus | ESCC | 8.71e-03 | 1.37e-01 | 0.0667 |
| 54059 | YBEY | LZE24T | Human | Esophagus | ESCC | 1.64e-07 | 3.54e-01 | 0.0596 |
| 54059 | YBEY | LZE6T | Human | Esophagus | ESCC | 1.79e-06 | 3.31e-01 | 0.0845 |
| 54059 | YBEY | P1T-E | Human | Esophagus | ESCC | 1.02e-03 | 1.31e-01 | 0.0875 |
| 54059 | YBEY | P2T-E | Human | Esophagus | ESCC | 1.18e-11 | 7.35e-02 | 0.1177 |
| 54059 | YBEY | P4T-E | Human | Esophagus | ESCC | 2.62e-32 | 7.72e-01 | 0.1323 |
| 54059 | YBEY | P5T-E | Human | Esophagus | ESCC | 9.49e-27 | 4.82e-01 | 0.1327 |
| 54059 | YBEY | P8T-E | Human | Esophagus | ESCC | 8.04e-11 | 4.73e-02 | 0.0889 |
| 54059 | YBEY | P9T-E | Human | Esophagus | ESCC | 9.67e-13 | 2.44e-01 | 0.1131 |
| 54059 | YBEY | P10T-E | Human | Esophagus | ESCC | 4.70e-32 | 4.43e-01 | 0.116 |
| 54059 | YBEY | P11T-E | Human | Esophagus | ESCC | 9.04e-04 | 6.07e-02 | 0.1426 |
| 54059 | YBEY | P12T-E | Human | Esophagus | ESCC | 3.95e-15 | 2.55e-01 | 0.1122 |
| 54059 | YBEY | P15T-E | Human | Esophagus | ESCC | 3.16e-08 | 1.00e-01 | 0.1149 |
| 54059 | YBEY | P16T-E | Human | Esophagus | ESCC | 2.96e-16 | 2.73e-01 | 0.1153 |
| 54059 | YBEY | P20T-E | Human | Esophagus | ESCC | 4.33e-10 | 1.78e-01 | 0.1124 |
| 54059 | YBEY | P21T-E | Human | Esophagus | ESCC | 1.50e-13 | 1.72e-01 | 0.1617 |
| 54059 | YBEY | P22T-E | Human | Esophagus | ESCC | 2.05e-21 | 2.88e-01 | 0.1236 |
| 54059 | YBEY | P23T-E | Human | Esophagus | ESCC | 3.06e-23 | 6.92e-01 | 0.108 |
| 54059 | YBEY | P24T-E | Human | Esophagus | ESCC | 4.62e-19 | 3.03e-01 | 0.1287 |
| 54059 | YBEY | P26T-E | Human | Esophagus | ESCC | 1.63e-25 | 2.89e-01 | 0.1276 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
| GO:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
| GO:004225412 | Liver | Cirrhotic | ribosome biogenesis | 154/4634 | 299/18723 | 1.18e-23 | 6.72e-21 | 154 |
| GO:000636412 | Liver | Cirrhotic | rRNA processing | 115/4634 | 225/18723 | 1.12e-17 | 1.64e-15 | 115 |
| GO:00160724 | Liver | Cirrhotic | rRNA metabolic process | 119/4634 | 236/18723 | 1.19e-17 | 1.70e-15 | 119 |
| GO:00344701 | Liver | Cirrhotic | ncRNA processing | 158/4634 | 395/18723 | 1.09e-11 | 6.96e-10 | 158 |
| GO:00346603 | Liver | Cirrhotic | ncRNA metabolic process | 173/4634 | 485/18723 | 3.64e-08 | 1.21e-06 | 173 |
| GO:0090501 | Liver | Cirrhotic | RNA phosphodiester bond hydrolysis | 54/4634 | 152/18723 | 1.89e-03 | 1.19e-02 | 54 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| YBEY | SNV | Missense_Mutation | novel | c.200C>T | p.Pro67Leu | p.P67L | P58557 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| YBEY | insertion | Frame_Shift_Ins | novel | c.174_175insCCTTTTCTCTGGGAACCGCTCCTTCCGCTCCGCCC | p.Val59ProfsTer26 | p.V59Pfs*26 | P58557 | protein_coding | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | ||
| YBEY | SNV | Missense_Mutation | c.247N>G | p.Pro83Ala | p.P83A | P58557 | protein_coding | tolerated(0.4) | benign(0.018) | TCGA-EK-A2R8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| YBEY | SNV | Missense_Mutation | c.17N>C | p.Arg6Thr | p.R6T | P58557 | protein_coding | deleterious(0) | possibly_damaging(0.815) | TCGA-FU-A3HY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| YBEY | SNV | Missense_Mutation | c.5N>T | p.Ser2Ile | p.S2I | P58557 | protein_coding | deleterious(0) | possibly_damaging(0.891) | TCGA-3L-AA1B-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| YBEY | SNV | Missense_Mutation | novel | c.312N>C | p.Glu104Asp | p.E104D | P58557 | protein_coding | tolerated(0.11) | benign(0.038) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| YBEY | SNV | Missense_Mutation | c.452G>A | p.Arg151His | p.R151H | P58557 | protein_coding | tolerated(0.6) | benign(0) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| YBEY | SNV | Missense_Mutation | novel | c.277N>A | p.Leu93Ile | p.L93I | P58557 | protein_coding | tolerated(0.06) | possibly_damaging(0.617) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| YBEY | SNV | Missense_Mutation | novel | c.101A>C | p.Lys34Thr | p.K34T | P58557 | protein_coding | tolerated(0.11) | benign(0.015) | TCGA-EY-A1G8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| YBEY | SNV | Missense_Mutation | novel | c.323A>G | p.Tyr108Cys | p.Y108C | P58557 | protein_coding | deleterious(0.01) | possibly_damaging(0.855) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
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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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