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Gene: LDB1 |
Gene summary for LDB1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LDB1 | Gene ID | 8861 |
| Gene name | LIM domain binding 1 | |
| Gene Alias | CLIM-2 | |
| Cytomap | 10q24.32 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q86U70 |
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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 |
| 8861 | LDB1 | LZE24T | Human | Esophagus | ESCC | 4.84e-09 | 1.80e-01 | 0.0596 |
| 8861 | LDB1 | P1T-E | Human | Esophagus | ESCC | 1.01e-07 | 2.67e-01 | 0.0875 |
| 8861 | LDB1 | P2T-E | Human | Esophagus | ESCC | 9.33e-24 | 4.69e-01 | 0.1177 |
| 8861 | LDB1 | P4T-E | Human | Esophagus | ESCC | 1.65e-22 | 4.98e-01 | 0.1323 |
| 8861 | LDB1 | P5T-E | Human | Esophagus | ESCC | 7.45e-13 | 2.62e-01 | 0.1327 |
| 8861 | LDB1 | P8T-E | Human | Esophagus | ESCC | 2.82e-04 | 1.03e-01 | 0.0889 |
| 8861 | LDB1 | P9T-E | Human | Esophagus | ESCC | 2.09e-02 | 4.12e-02 | 0.1131 |
| 8861 | LDB1 | P10T-E | Human | Esophagus | ESCC | 1.28e-03 | 7.17e-02 | 0.116 |
| 8861 | LDB1 | P11T-E | Human | Esophagus | ESCC | 3.74e-07 | 3.03e-01 | 0.1426 |
| 8861 | LDB1 | P12T-E | Human | Esophagus | ESCC | 2.42e-26 | 5.41e-01 | 0.1122 |
| 8861 | LDB1 | P15T-E | Human | Esophagus | ESCC | 1.22e-25 | 4.02e-01 | 0.1149 |
| 8861 | LDB1 | P16T-E | Human | Esophagus | ESCC | 8.84e-09 | 2.37e-01 | 0.1153 |
| 8861 | LDB1 | P17T-E | Human | Esophagus | ESCC | 1.03e-07 | 2.08e-01 | 0.1278 |
| 8861 | LDB1 | P20T-E | Human | Esophagus | ESCC | 1.92e-15 | 2.73e-01 | 0.1124 |
| 8861 | LDB1 | P21T-E | Human | Esophagus | ESCC | 2.04e-06 | 9.54e-02 | 0.1617 |
| 8861 | LDB1 | P22T-E | Human | Esophagus | ESCC | 5.92e-06 | 1.15e-01 | 0.1236 |
| 8861 | LDB1 | P23T-E | Human | Esophagus | ESCC | 5.78e-07 | 1.96e-01 | 0.108 |
| 8861 | LDB1 | P26T-E | Human | Esophagus | ESCC | 1.26e-21 | 3.63e-01 | 0.1276 |
| 8861 | LDB1 | P27T-E | Human | Esophagus | ESCC | 8.05e-13 | 2.98e-01 | 0.1055 |
| 8861 | LDB1 | P28T-E | Human | Esophagus | ESCC | 1.56e-17 | 3.22e-01 | 0.1149 |
| 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 | ||
| 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 |
| ∗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:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:001820514 | Esophagus | ESCC | peptidyl-lysine modification | 259/8552 | 376/18723 | 3.90e-20 | 5.26e-18 | 259 |
| GO:000635414 | Esophagus | ESCC | DNA-templated transcription, elongation | 76/8552 | 91/18723 | 8.35e-14 | 4.11e-12 | 76 |
| GO:001839413 | Esophagus | ESCC | peptidyl-lysine acetylation | 123/8552 | 169/18723 | 6.58e-13 | 2.94e-11 | 123 |
| GO:004354313 | Esophagus | ESCC | protein acylation | 165/8552 | 243/18723 | 1.69e-12 | 7.14e-11 | 165 |
| GO:000647313 | Esophagus | ESCC | protein acetylation | 140/8552 | 201/18723 | 4.37e-12 | 1.69e-10 | 140 |
| GO:001839313 | Esophagus | ESCC | internal peptidyl-lysine acetylation | 114/8552 | 158/18723 | 1.16e-11 | 4.24e-10 | 114 |
| GO:000647513 | Esophagus | ESCC | internal protein amino acid acetylation | 115/8552 | 160/18723 | 1.43e-11 | 5.08e-10 | 115 |
| GO:00165735 | Esophagus | ESCC | histone acetylation | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:001605517 | Esophagus | ESCC | Wnt signaling pathway | 268/8552 | 444/18723 | 2.32e-10 | 6.58e-09 | 268 |
| GO:019873817 | Esophagus | ESCC | cell-cell signaling by wnt | 269/8552 | 446/18723 | 2.41e-10 | 6.79e-09 | 269 |
| GO:0150115110 | Esophagus | ESCC | cell-substrate junction organization | 77/8552 | 101/18723 | 3.46e-10 | 9.57e-09 | 77 |
| GO:000704418 | Esophagus | ESCC | cell-substrate junction assembly | 73/8552 | 95/18723 | 5.27e-10 | 1.35e-08 | 73 |
| GO:0030099111 | Esophagus | ESCC | myeloid cell differentiation | 232/8552 | 381/18723 | 1.22e-09 | 2.90e-08 | 232 |
| GO:000636814 | Esophagus | ESCC | transcription elongation from RNA polymerase II promoter | 56/8552 | 69/18723 | 1.40e-09 | 3.30e-08 | 56 |
| GO:003158919 | Esophagus | ESCC | cell-substrate adhesion | 221/8552 | 363/18723 | 3.06e-09 | 6.62e-08 | 221 |
| GO:001081020 | Esophagus | ESCC | regulation of cell-substrate adhesion | 144/8552 | 221/18723 | 3.55e-09 | 7.45e-08 | 144 |
| GO:003278412 | Esophagus | ESCC | regulation of DNA-templated transcription, elongation | 45/8552 | 53/18723 | 3.64e-09 | 7.61e-08 | 45 |
| GO:004804116 | Esophagus | ESCC | focal adhesion assembly | 65/8552 | 87/18723 | 3.28e-08 | 6.08e-07 | 65 |
| GO:004578527 | Esophagus | ESCC | positive regulation of cell adhesion | 255/8552 | 437/18723 | 5.07e-08 | 9.11e-07 | 255 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052028 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0520213 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0520221 | Prostate | Tumor | Transcriptional misregulation in cancer | 59/1791 | 193/8465 | 1.22e-03 | 5.26e-03 | 3.26e-03 | 59 |
| hsa0520231 | Prostate | Tumor | Transcriptional misregulation in cancer | 59/1791 | 193/8465 | 1.22e-03 | 5.26e-03 | 3.26e-03 | 59 |
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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. |
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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 |
| LDB1 | SNV | Missense_Mutation | c.301G>C | p.Asp101His | p.D101H | Q86U70 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| LDB1 | SNV | Missense_Mutation | c.547N>C | p.Tyr183His | p.Y183H | Q86U70 | protein_coding | deleterious(0.05) | probably_damaging(0.995) | TCGA-A8-A08O-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | PD | |
| LDB1 | insertion | Nonsense_Mutation | novel | c.610_611insTCGGTGTGGGCTGTCCAATTCCACTCTCAACTACCTCCGAGTG | p.His204LeufsTer15 | p.H204Lfs*15 | Q86U70 | protein_coding | TCGA-BH-A0BR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LDB1 | SNV | Missense_Mutation | novel | c.800G>A | p.Arg267His | p.R267H | Q86U70 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LDB1 | SNV | Missense_Mutation | c.578G>A | p.Arg193Gln | p.R193Q | Q86U70 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LDB1 | SNV | Missense_Mutation | rs768693158 | c.985G>A | p.Ala329Thr | p.A329T | Q86U70 | protein_coding | tolerated(0.13) | benign(0.058) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| LDB1 | SNV | Missense_Mutation | rs751950349 | c.1057G>A | p.Glu353Lys | p.E353K | Q86U70 | protein_coding | deleterious(0.02) | possibly_damaging(0.905) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LDB1 | SNV | Missense_Mutation | rs768693158 | c.985G>A | p.Ala329Thr | p.A329T | Q86U70 | protein_coding | tolerated(0.13) | benign(0.058) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| LDB1 | SNV | Missense_Mutation | rs767872374 | c.376N>T | p.Arg126Cys | p.R126C | Q86U70 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LDB1 | SNV | Missense_Mutation | c.291N>A | p.Phe97Leu | p.F97L | Q86U70 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| Page: 1 2 3 4 |
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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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