|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: LDB3 |
Gene summary for LDB3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LDB3 | Gene ID | 11155 |
| Gene name | LIM domain binding 3 | |
| Gene Alias | CMD1C | |
| Cytomap | 10q23.2 | |
| Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | O75112 |
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 |
| 11155 | LDB3 | HCC1 | Human | Liver | HCC | 2.10e-06 | 5.47e-01 | 0.5336 |
| 11155 | LDB3 | HCC2 | Human | Liver | HCC | 2.08e-08 | 4.60e-01 | 0.5341 |
| 11155 | LDB3 | HCC5 | Human | Liver | HCC | 1.23e-09 | 7.44e-01 | 0.4932 |
| 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:003103222 | Liver | HCC | actomyosin structure organization | 109/7958 | 196/18723 | 1.39e-04 | 1.13e-03 | 109 |
| 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 |
| LDB3 | SNV | Missense_Mutation | novel | c.1748N>T | p.Ala583Val | p.A583V | O75112 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| LDB3 | SNV | Missense_Mutation | c.995N>T | p.Ala332Val | p.A332V | O75112 | protein_coding | tolerated(0.19) | benign(0.084) | TCGA-A2-A0YH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| LDB3 | SNV | Missense_Mutation | c.1535N>T | p.Thr512Ile | p.T512I | O75112 | protein_coding | deleterious(0) | benign(0.368) | TCGA-A2-A1FW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| LDB3 | SNV | Missense_Mutation | rs747011937 | c.1109N>T | p.Ala370Val | p.A370V | O75112 | protein_coding | tolerated(0.39) | benign(0.015) | TCGA-AC-A2FG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | CR |
| LDB3 | insertion | Frame_Shift_Ins | novel | c.78_79insAATT | p.Leu27AsnfsTer22 | p.L27Nfs*22 | O75112 | protein_coding | TCGA-A2-A04U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| LDB3 | insertion | Nonsense_Mutation | novel | c.80_81insTCTCCAATAACACCTGACCACACGTCGCA | p.Thr28LeufsTer3 | p.T28Lfs*3 | O75112 | protein_coding | TCGA-A2-A04U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| LDB3 | deletion | Frame_Shift_Del | novel | c.1053delG | p.Thr352GlnfsTer145 | p.T352Qfs*145 | O75112 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| LDB3 | SNV | Missense_Mutation | c.627N>C | p.Glu209Asp | p.E209D | O75112 | protein_coding | tolerated(0.32) | probably_damaging(0.978) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| LDB3 | SNV | Missense_Mutation | novel | c.373N>C | p.Glu125Gln | p.E125Q | O75112 | protein_coding | tolerated(0.41) | benign(0.017) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| LDB3 | SNV | Missense_Mutation | c.1889N>C | p.Leu630Ser | p.L630S | O75112 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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 |