|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: LRRC2 |
Gene summary for LRRC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LRRC2 | Gene ID | 79442 |
| Gene name | leucine rich repeat containing 2 | |
| Gene Alias | LRRC2 | |
| Cytomap | 3p21.31 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | A0A024R2R5 |
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 |
| 79442 | LRRC2 | HCC1 | Human | Liver | HCC | 1.41e-10 | 1.74e+00 | 0.5336 |
| 79442 | LRRC2 | HCC2 | Human | Liver | HCC | 8.98e-40 | 3.83e+00 | 0.5341 |
| 79442 | LRRC2 | HCC5 | Human | Liver | HCC | 6.59e-23 | 1.61e+00 | 0.4932 |
| 79442 | LRRC2 | Adj_PTCwithHT_6 | Human | Thyroid | HT | 1.09e-02 | -2.47e-01 | 0.02 |
| 79442 | LRRC2 | PTCwithHT_6 | Human | Thyroid | HT | 1.25e-05 | -2.42e-01 | 0.02 |
| 79442 | LRRC2 | male-WTA | Human | Thyroid | PTC | 7.49e-12 | -1.32e-01 | 0.1037 |
| 79442 | LRRC2 | PTC01 | Human | Thyroid | PTC | 8.75e-08 | -8.26e-02 | 0.1899 |
| 79442 | LRRC2 | PTC04 | Human | Thyroid | PTC | 8.07e-15 | 1.03e-01 | 0.1927 |
| 79442 | LRRC2 | PTC05 | Human | Thyroid | PTC | 2.11e-07 | 2.35e-02 | 0.2065 |
| 79442 | LRRC2 | PTC06 | Human | Thyroid | PTC | 5.19e-11 | -5.72e-02 | 0.2057 |
| 79442 | LRRC2 | PTC07 | Human | Thyroid | PTC | 2.22e-15 | 4.49e-02 | 0.2044 |
| 79442 | LRRC2 | ATC12 | Human | Thyroid | ATC | 4.38e-02 | -2.48e-01 | 0.34 |
| 79442 | LRRC2 | ATC13 | Human | Thyroid | ATC | 1.84e-06 | -2.07e-01 | 0.34 |
| 79442 | LRRC2 | ATC4 | Human | Thyroid | ATC | 2.33e-04 | -2.42e-01 | 0.34 |
| 79442 | LRRC2 | ATC5 | Human | Thyroid | ATC | 1.31e-02 | -2.04e-01 | 0.34 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:00324116 | Breast | Precancer | positive regulation of transporter activity | 16/1080 | 120/18723 | 1.46e-03 | 1.51e-02 | 16 |
| GO:00347673 | Breast | Precancer | positive regulation of ion transmembrane transport | 19/1080 | 167/18723 | 3.60e-03 | 2.98e-02 | 19 |
| GO:00324143 | Breast | Precancer | positive regulation of ion transmembrane transporter activity | 14/1080 | 109/18723 | 3.97e-03 | 3.15e-02 | 14 |
| GO:00109596 | Breast | Precancer | regulation of metal ion transport | 37/1080 | 406/18723 | 4.07e-03 | 3.22e-02 | 37 |
| GO:00228985 | Breast | Precancer | regulation of transmembrane transporter activity | 27/1080 | 278/18723 | 5.72e-03 | 4.11e-02 | 27 |
| GO:001095913 | Breast | IDC | regulation of metal ion transport | 52/1434 | 406/18723 | 1.76e-04 | 2.97e-03 | 52 |
| GO:003241111 | Breast | IDC | positive regulation of transporter activity | 20/1434 | 120/18723 | 7.64e-04 | 9.27e-03 | 20 |
| GO:00432703 | Breast | IDC | positive regulation of ion transport | 36/1434 | 275/18723 | 1.11e-03 | 1.22e-02 | 36 |
| GO:002289812 | Breast | IDC | regulation of transmembrane transporter activity | 36/1434 | 278/18723 | 1.35e-03 | 1.40e-02 | 36 |
| GO:003241411 | Breast | IDC | positive regulation of ion transmembrane transporter activity | 18/1434 | 109/18723 | 1.53e-03 | 1.53e-02 | 18 |
| GO:003476711 | Breast | IDC | positive regulation of ion transmembrane transport | 24/1434 | 167/18723 | 2.07e-03 | 1.95e-02 | 24 |
| GO:00324125 | Breast | IDC | regulation of ion transmembrane transporter activity | 33/1434 | 267/18723 | 4.38e-03 | 3.40e-02 | 33 |
| GO:00324096 | Breast | IDC | regulation of transporter activity | 37/1434 | 310/18723 | 4.77e-03 | 3.66e-02 | 37 |
| GO:00347644 | Breast | IDC | positive regulation of transmembrane transport | 28/1434 | 219/18723 | 5.19e-03 | 3.86e-02 | 28 |
| GO:001095921 | Breast | DCIS | regulation of metal ion transport | 50/1390 | 406/18723 | 2.86e-04 | 4.22e-03 | 50 |
| GO:003241121 | Breast | DCIS | positive regulation of transporter activity | 20/1390 | 120/18723 | 5.16e-04 | 6.73e-03 | 20 |
| GO:003241421 | Breast | DCIS | positive regulation of ion transmembrane transporter activity | 18/1390 | 109/18723 | 1.07e-03 | 1.17e-02 | 18 |
| GO:003476721 | Breast | DCIS | positive regulation of ion transmembrane transport | 24/1390 | 167/18723 | 1.37e-03 | 1.42e-02 | 24 |
| GO:002289822 | Breast | DCIS | regulation of transmembrane transporter activity | 35/1390 | 278/18723 | 1.50e-03 | 1.51e-02 | 35 |
| GO:004327011 | Breast | DCIS | positive regulation of ion transport | 34/1390 | 275/18723 | 2.35e-03 | 2.13e-02 | 34 |
| Page: 1 2 |
| 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 |
| LRRC2 | SNV | Missense_Mutation | c.1076N>T | p.Pro359Leu | p.P359L | Q9BYS8 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-D8-A1XY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | tamoxiphen | SD | |
| LRRC2 | insertion | Nonsense_Mutation | novel | c.411_412insGGGTGGTGAGGTCGGCGTCTCGCCTGTATAACTCAGCACATAGG | p.Thr138GlyfsTer3 | p.T138Gfs*3 | Q9BYS8 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| LRRC2 | insertion | Frame_Shift_Ins | novel | c.268_269insCCTCCGTCCATCTCTTTGTATCT | p.Leu90ProfsTer36 | p.L90Pfs*36 | Q9BYS8 | protein_coding | TCGA-AO-A0JF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD | ||
| LRRC2 | insertion | In_Frame_Ins | novel | c.266_267insCCTGGG | p.Leu90_Pro91insGlyLeu | p.L90_P91insGL | Q9BYS8 | protein_coding | TCGA-AO-A0JF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD | ||
| LRRC2 | SNV | Missense_Mutation | novel | c.631N>G | p.Ser211Gly | p.S211G | Q9BYS8 | protein_coding | deleterious(0.01) | probably_damaging(0.985) | TCGA-C5-A901-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LRRC2 | SNV | Missense_Mutation | novel | c.562N>C | p.Asp188His | p.D188H | Q9BYS8 | protein_coding | tolerated(0.05) | benign(0.09) | TCGA-VS-A9UH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LRRC2 | SNV | Missense_Mutation | c.980G>A | p.Gly327Asp | p.G327D | Q9BYS8 | protein_coding | tolerated(0.62) | benign(0) | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | |
| LRRC2 | SNV | Missense_Mutation | c.1068A>T | p.Glu356Asp | p.E356D | Q9BYS8 | protein_coding | tolerated(0.63) | benign(0.001) | TCGA-AA-3815-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LRRC2 | SNV | Missense_Mutation | c.932N>C | p.Phe311Ser | p.F311S | Q9BYS8 | protein_coding | deleterious(0) | benign(0.282) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| LRRC2 | SNV | Missense_Mutation | rs752406824 | c.154N>A | p.Glu52Lys | p.E52K | Q9BYS8 | protein_coding | tolerated(0.09) | probably_damaging(0.98) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | 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 |