|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: LRRC47 |
Gene summary for LRRC47 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LRRC47 | Gene ID | 57470 |
| Gene name | leucine rich repeat containing 47 | |
| Gene Alias | LRRC47 | |
| Cytomap | 1p36.32 | |
| Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | A0A024R4G1 |
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 |
| 57470 | LRRC47 | LZE7T | Human | Esophagus | ESCC | 7.07e-05 | 1.78e-01 | 0.0667 |
| 57470 | LRRC47 | LZE20T | Human | Esophagus | ESCC | 7.55e-03 | 1.80e-01 | 0.0662 |
| 57470 | LRRC47 | LZE22T | Human | Esophagus | ESCC | 7.76e-04 | 4.68e-01 | 0.068 |
| 57470 | LRRC47 | LZE24T | Human | Esophagus | ESCC | 2.66e-17 | 3.91e-01 | 0.0596 |
| 57470 | LRRC47 | P1T-E | Human | Esophagus | ESCC | 2.74e-07 | 4.24e-01 | 0.0875 |
| 57470 | LRRC47 | P2T-E | Human | Esophagus | ESCC | 3.86e-41 | 7.12e-01 | 0.1177 |
| 57470 | LRRC47 | P4T-E | Human | Esophagus | ESCC | 3.51e-32 | 8.76e-01 | 0.1323 |
| 57470 | LRRC47 | P5T-E | Human | Esophagus | ESCC | 2.44e-18 | 2.72e-01 | 0.1327 |
| 57470 | LRRC47 | P8T-E | Human | Esophagus | ESCC | 3.06e-51 | 9.02e-01 | 0.0889 |
| 57470 | LRRC47 | P9T-E | Human | Esophagus | ESCC | 4.50e-11 | 2.56e-01 | 0.1131 |
| 57470 | LRRC47 | P10T-E | Human | Esophagus | ESCC | 2.23e-39 | 6.86e-01 | 0.116 |
| 57470 | LRRC47 | P11T-E | Human | Esophagus | ESCC | 1.11e-14 | 7.37e-01 | 0.1426 |
| 57470 | LRRC47 | P12T-E | Human | Esophagus | ESCC | 2.17e-27 | 5.73e-01 | 0.1122 |
| 57470 | LRRC47 | P15T-E | Human | Esophagus | ESCC | 1.51e-28 | 6.93e-01 | 0.1149 |
| 57470 | LRRC47 | P16T-E | Human | Esophagus | ESCC | 7.32e-29 | 5.28e-01 | 0.1153 |
| 57470 | LRRC47 | P17T-E | Human | Esophagus | ESCC | 5.63e-05 | 5.02e-01 | 0.1278 |
| 57470 | LRRC47 | P19T-E | Human | Esophagus | ESCC | 2.58e-04 | 7.42e-01 | 0.1662 |
| 57470 | LRRC47 | P20T-E | Human | Esophagus | ESCC | 4.06e-25 | 6.52e-01 | 0.1124 |
| 57470 | LRRC47 | P21T-E | Human | Esophagus | ESCC | 3.07e-33 | 6.83e-01 | 0.1617 |
| 57470 | LRRC47 | P22T-E | Human | Esophagus | ESCC | 4.03e-14 | 2.32e-01 | 0.1236 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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. |
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:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:00065202 | Liver | HCC | cellular amino acid metabolic process | 167/7958 | 284/18723 | 1.91e-08 | 4.56e-07 | 167 |
| GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
| GO:00346605 | Oral cavity | OSCC | ncRNA metabolic process | 296/7305 | 485/18723 | 2.94e-23 | 6.65e-21 | 296 |
| GO:00063991 | Oral cavity | OSCC | tRNA metabolic process | 101/7305 | 179/18723 | 1.65e-06 | 2.15e-05 | 101 |
| GO:003466011 | Oral cavity | LP | ncRNA metabolic process | 205/4623 | 485/18723 | 6.46e-18 | 1.09e-15 | 205 |
| GO:003466013 | Skin | cSCC | ncRNA metabolic process | 234/4864 | 485/18723 | 1.37e-26 | 4.77e-24 | 234 |
| GO:00063993 | Skin | cSCC | tRNA metabolic process | 64/4864 | 179/18723 | 2.34e-03 | 1.36e-02 | 64 |
| GO:00346608 | Thyroid | PTC | ncRNA metabolic process | 239/5968 | 485/18723 | 5.54e-16 | 4.26e-14 | 239 |
| GO:003466021 | Thyroid | ATC | ncRNA metabolic process | 240/6293 | 485/18723 | 2.03e-13 | 9.91e-12 | 240 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| LRRC47 | SNV | Missense_Mutation | c.1573G>A | p.Asp525Asn | p.D525N | Q8N1G4 | protein_coding | tolerated(0.1) | benign(0.003) | TCGA-B6-A0WZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| LRRC47 | SNV | Missense_Mutation | novel | c.904N>A | p.Gly302Arg | p.G302R | Q8N1G4 | protein_coding | tolerated(0.27) | benign(0.034) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LRRC47 | SNV | Missense_Mutation | c.629N>G | p.Ser210Trp | p.S210W | Q8N1G4 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-BH-A0HN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| LRRC47 | SNV | Missense_Mutation | c.1700N>G | p.Pro567Arg | p.P567R | Q8N1G4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A1F6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| LRRC47 | SNV | Missense_Mutation | rs760459981 | c.1025N>A | p.Arg342Gln | p.R342Q | Q8N1G4 | protein_coding | deleterious(0.03) | possibly_damaging(0.45) | TCGA-C5-A1MK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
| LRRC47 | SNV | Missense_Mutation | rs778807067 | c.1261G>A | p.Glu421Lys | p.E421K | Q8N1G4 | protein_coding | deleterious(0) | possibly_damaging(0.726) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| LRRC47 | SNV | Missense_Mutation | rs750487355 | c.665N>T | p.Ala222Val | p.A222V | Q8N1G4 | protein_coding | deleterious(0.01) | possibly_damaging(0.866) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LRRC47 | SNV | Missense_Mutation | rs772851625 | c.982G>A | p.Glu328Lys | p.E328K | Q8N1G4 | protein_coding | tolerated(0.52) | benign(0.062) | TCGA-MY-A5BD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LRRC47 | SNV | Missense_Mutation | c.1073C>T | p.Ser358Leu | p.S358L | Q8N1G4 | protein_coding | tolerated(0.72) | benign(0.01) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LRRC47 | SNV | Missense_Mutation | c.1505A>C | p.Lys502Thr | p.K502T | Q8N1G4 | protein_coding | deleterious(0) | possibly_damaging(0.79) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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 |