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Gene: LTBP4 |
Gene summary for LTBP4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LTBP4 | Gene ID | 8425 |
| Gene name | latent transforming growth factor beta binding protein 4 | |
| Gene Alias | ARCL1C | |
| Cytomap | 19q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0001558 | UniProtAcc | B3KXY6 |
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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 |
| 8425 | LTBP4 | AEH-subject1 | Human | Endometrium | AEH | 1.71e-37 | -6.89e-01 | -0.3059 |
| 8425 | LTBP4 | AEH-subject2 | Human | Endometrium | AEH | 2.06e-13 | -5.08e-01 | -0.2525 |
| 8425 | LTBP4 | AEH-subject3 | Human | Endometrium | AEH | 9.13e-24 | -6.14e-01 | -0.2576 |
| 8425 | LTBP4 | AEH-subject4 | Human | Endometrium | AEH | 1.18e-16 | -5.80e-01 | -0.2657 |
| 8425 | LTBP4 | AEH-subject5 | Human | Endometrium | AEH | 3.18e-32 | -7.12e-01 | -0.2953 |
| 8425 | LTBP4 | EEC-subject1 | Human | Endometrium | EEC | 5.85e-30 | -7.23e-01 | -0.2682 |
| 8425 | LTBP4 | EEC-subject2 | Human | Endometrium | EEC | 1.38e-24 | -6.37e-01 | -0.2607 |
| 8425 | LTBP4 | EEC-subject3 | Human | Endometrium | EEC | 7.50e-37 | -6.77e-01 | -0.2525 |
| 8425 | LTBP4 | EEC-subject4 | Human | Endometrium | EEC | 1.75e-24 | -6.19e-01 | -0.2571 |
| 8425 | LTBP4 | EEC-subject5 | Human | Endometrium | EEC | 2.74e-42 | -7.35e-01 | -0.249 |
| 8425 | LTBP4 | GSM5276935 | Human | Endometrium | EEC | 4.33e-43 | -7.54e-01 | -0.123 |
| 8425 | LTBP4 | GSM5276937 | Human | Endometrium | EEC | 1.79e-03 | -3.37e-01 | -0.0897 |
| 8425 | LTBP4 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.28e-34 | -7.58e-01 | -0.1869 |
| 8425 | LTBP4 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 7.73e-31 | -7.56e-01 | -0.1875 |
| 8425 | LTBP4 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 1.02e-35 | -7.60e-01 | -0.1883 |
| 8425 | LTBP4 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.08e-29 | -6.00e-01 | -0.1934 |
| 8425 | LTBP4 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 2.68e-38 | -6.98e-01 | -0.1917 |
| 8425 | LTBP4 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 7.53e-39 | -7.21e-01 | -0.1916 |
| 8425 | LTBP4 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 1.76e-30 | -7.11e-01 | -0.1269 |
| 8425 | LTBP4 | LZE4T | Human | Esophagus | ESCC | 1.61e-10 | 1.03e-02 | 0.0811 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| 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. |
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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:000645710 | Endometrium | AEH | protein folding | 61/2100 | 212/18723 | 1.86e-12 | 3.48e-10 | 61 |
| GO:00160499 | Endometrium | AEH | cell growth | 93/2100 | 482/18723 | 1.00e-07 | 4.99e-06 | 93 |
| GO:00715596 | Endometrium | AEH | response to transforming growth factor beta | 53/2100 | 256/18723 | 7.01e-06 | 1.69e-04 | 53 |
| GO:00071787 | Endometrium | AEH | transmembrane receptor protein serine/threonine kinase signaling pathway | 67/2100 | 355/18723 | 1.28e-05 | 2.80e-04 | 67 |
| GO:00715606 | Endometrium | AEH | cellular response to transforming growth factor beta stimulus | 51/2100 | 250/18723 | 1.59e-05 | 3.32e-04 | 51 |
| GO:00015589 | Endometrium | AEH | regulation of cell growth | 75/2100 | 414/18723 | 1.79e-05 | 3.65e-04 | 75 |
| GO:00071796 | Endometrium | AEH | transforming growth factor beta receptor signaling pathway | 38/2100 | 198/18723 | 6.41e-04 | 6.23e-03 | 38 |
| GO:00900922 | Endometrium | AEH | regulation of transmembrane receptor protein serine/threonine kinase signaling pathway | 43/2100 | 256/18723 | 4.47e-03 | 2.93e-02 | 43 |
| GO:000645715 | Endometrium | EEC | protein folding | 63/2168 | 212/18723 | 6.82e-13 | 1.40e-10 | 63 |
| GO:001604915 | Endometrium | EEC | cell growth | 95/2168 | 482/18723 | 1.16e-07 | 5.54e-06 | 95 |
| GO:007155914 | Endometrium | EEC | response to transforming growth factor beta | 54/2168 | 256/18723 | 8.25e-06 | 1.83e-04 | 54 |
| GO:000155814 | Endometrium | EEC | regulation of cell growth | 77/2168 | 414/18723 | 1.64e-05 | 3.16e-04 | 77 |
| GO:007156014 | Endometrium | EEC | cellular response to transforming growth factor beta stimulus | 52/2168 | 250/18723 | 1.81e-05 | 3.41e-04 | 52 |
| GO:000717814 | Endometrium | EEC | transmembrane receptor protein serine/threonine kinase signaling pathway | 68/2168 | 355/18723 | 1.90e-05 | 3.50e-04 | 68 |
| GO:000717914 | Endometrium | EEC | transforming growth factor beta receptor signaling pathway | 39/2168 | 198/18723 | 6.03e-04 | 5.98e-03 | 39 |
| GO:009009211 | Endometrium | EEC | regulation of transmembrane receptor protein serine/threonine kinase signaling pathway | 44/2168 | 256/18723 | 4.72e-03 | 3.00e-02 | 44 |
| GO:0006457110 | Esophagus | ESCC | protein folding | 163/8552 | 212/18723 | 1.13e-20 | 1.74e-18 | 163 |
| GO:0016049110 | Esophagus | ESCC | cell growth | 289/8552 | 482/18723 | 1.29e-10 | 3.77e-09 | 289 |
| GO:000155819 | Esophagus | ESCC | regulation of cell growth | 248/8552 | 414/18723 | 2.97e-09 | 6.45e-08 | 248 |
| GO:00715599 | Esophagus | ESCC | response to transforming growth factor beta | 157/8552 | 256/18723 | 2.95e-07 | 4.23e-06 | 157 |
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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 |
| LTBP4 | SNV | Missense_Mutation | rs776226657 | c.2903G>A | p.Arg968Gln | p.R968Q | Q8N2S1 | protein_coding | tolerated(0.33) | possibly_damaging(0.792) | TCGA-A2-A1FV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | SD |
| LTBP4 | SNV | Missense_Mutation | novel | c.1721N>G | p.Ser574Cys | p.S574C | Q8N2S1 | protein_coding | deleterious(0.03) | benign(0.41) | TCGA-A7-A4SF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| LTBP4 | SNV | Missense_Mutation | rs764846754 | c.3161N>A | p.Arg1054Gln | p.R1054Q | Q8N2S1 | protein_coding | tolerated(0.22) | probably_damaging(0.937) | TCGA-A8-A09B-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD |
| LTBP4 | SNV | Missense_Mutation | rs748078658 | c.3190G>A | p.Val1064Met | p.V1064M | Q8N2S1 | protein_coding | tolerated(0.22) | benign(0.031) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| LTBP4 | SNV | Missense_Mutation | rs759424524 | c.3614N>G | p.Glu1205Gly | p.E1205G | Q8N2S1 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LTBP4 | SNV | Missense_Mutation | novel | c.4691N>A | p.Arg1564His | p.R1564H | Q8N2S1 | protein_coding | tolerated(0.08) | possibly_damaging(0.866) | TCGA-B6-A402-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | PD |
| LTBP4 | SNV | Missense_Mutation | c.1495N>G | p.Arg499Gly | p.R499G | Q8N2S1 | protein_coding | tolerated(0.05) | benign(0.056) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| LTBP4 | SNV | Missense_Mutation | rs768448054 | c.2108N>A | p.Arg703Gln | p.R703Q | Q8N2S1 | protein_coding | tolerated(0.14) | benign(0.006) | TCGA-D8-A1Y2-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| LTBP4 | SNV | Missense_Mutation | novel | c.1520N>T | p.Thr507Ile | p.T507I | Q8N2S1 | protein_coding | tolerated(0.07) | possibly_damaging(0.878) | TCGA-D8-A27N-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol+adriamycin+cyclophosphamide+herceptin | SD |
| LTBP4 | SNV | Missense_Mutation | c.2051N>T | p.Arg684Leu | p.R684L | Q8N2S1 | protein_coding | deleterious(0.05) | benign(0.217) | TCGA-E2-A152-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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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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