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Gene: LTA |
Gene summary for LTA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LTA | Gene ID | 4049 |
| Gene name | lymphotoxin alpha | |
| Gene Alias | LT | |
| Cytomap | 6p21.33 | |
| Gene Type | protein-coding | GO ID | GO:0001666 | UniProtAcc | P01374 |
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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 |
| 4049 | LTA | LZE6T | Human | Esophagus | ESCC | 1.62e-02 | 1.56e-01 | 0.0845 |
| 4049 | LTA | P5T-E | Human | Esophagus | ESCC | 1.59e-30 | 5.40e-01 | 0.1327 |
| 4049 | LTA | P10T-E | Human | Esophagus | ESCC | 7.74e-41 | 6.11e-01 | 0.116 |
| 4049 | LTA | P22T-E | Human | Esophagus | ESCC | 1.07e-50 | 7.89e-01 | 0.1236 |
| 4049 | LTA | P23T-E | Human | Esophagus | ESCC | 1.52e-59 | 1.29e+00 | 0.108 |
| 4049 | LTA | P31T-E | Human | Esophagus | ESCC | 5.17e-27 | 4.44e-01 | 0.1251 |
| 4049 | LTA | P32T-E | Human | Esophagus | ESCC | 1.02e-31 | 5.55e-01 | 0.1666 |
| 4049 | LTA | P37T-E | Human | Esophagus | ESCC | 3.33e-64 | 1.16e+00 | 0.1371 |
| 4049 | LTA | P39T-E | Human | Esophagus | ESCC | 1.06e-41 | 7.01e-01 | 0.0894 |
| 4049 | LTA | P42T-E | Human | Esophagus | ESCC | 6.32e-23 | 5.31e-01 | 0.1175 |
| 4049 | LTA | P47T-E | Human | Esophagus | ESCC | 3.28e-14 | 2.83e-01 | 0.1067 |
| 4049 | LTA | P48T-E | Human | Esophagus | ESCC | 6.36e-33 | 5.74e-01 | 0.0959 |
| 4049 | LTA | P52T-E | Human | Esophagus | ESCC | 1.51e-34 | 6.57e-01 | 0.1555 |
| 4049 | LTA | P54T-E | Human | Esophagus | ESCC | 3.85e-45 | 8.90e-01 | 0.0975 |
| 4049 | LTA | P56T-E | Human | Esophagus | ESCC | 5.20e-23 | 1.49e+00 | 0.1613 |
| 4049 | LTA | P74T-E | Human | Esophagus | ESCC | 2.74e-71 | 1.61e+00 | 0.1479 |
| 4049 | LTA | P75T-E | Human | Esophagus | ESCC | 7.65e-86 | 1.44e+00 | 0.1125 |
| 4049 | LTA | P76T-E | Human | Esophagus | ESCC | 2.06e-58 | 9.30e-01 | 0.1207 |
| 4049 | LTA | P89T-E | Human | Esophagus | ESCC | 1.42e-31 | 1.75e+00 | 0.1752 |
| 4049 | LTA | P91T-E | Human | Esophagus | ESCC | 9.21e-26 | 1.79e+00 | 0.1828 |
| Page: 1 2 |
| 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 |
| ∗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:00068986 | Breast | Precancer | receptor-mediated endocytosis | 27/1080 | 244/18723 | 9.01e-04 | 1.03e-02 | 27 |
| GO:00482685 | Breast | Precancer | clathrin coat assembly | 5/1080 | 18/18723 | 2.88e-03 | 2.49e-02 | 5 |
| GO:000689813 | Breast | IDC | receptor-mediated endocytosis | 35/1434 | 244/18723 | 2.38e-04 | 3.75e-03 | 35 |
| GO:000689823 | Breast | DCIS | receptor-mediated endocytosis | 35/1390 | 244/18723 | 1.31e-04 | 2.25e-03 | 35 |
| GO:00068987 | Cervix | CC | receptor-mediated endocytosis | 53/2311 | 244/18723 | 2.52e-05 | 4.29e-04 | 53 |
| GO:00725836 | Cervix | CC | clathrin-dependent endocytosis | 16/2311 | 47/18723 | 9.56e-05 | 1.25e-03 | 16 |
| GO:00482686 | Cervix | CC | clathrin coat assembly | 7/2311 | 18/18723 | 3.99e-03 | 2.48e-02 | 7 |
| GO:000689824 | Cervix | N_HPV | receptor-mediated endocytosis | 17/534 | 244/18723 | 6.68e-04 | 8.57e-03 | 17 |
| GO:0072583 | Colorectum | AD | clathrin-dependent endocytosis | 24/3918 | 47/18723 | 4.60e-06 | 1.22e-04 | 24 |
| GO:0006898 | Colorectum | AD | receptor-mediated endocytosis | 76/3918 | 244/18723 | 1.07e-04 | 1.59e-03 | 76 |
| GO:0048268 | Colorectum | AD | clathrin coat assembly | 10/3918 | 18/18723 | 1.31e-03 | 1.15e-02 | 10 |
| GO:00725831 | Colorectum | MSS | clathrin-dependent endocytosis | 22/3467 | 47/18723 | 8.74e-06 | 2.16e-04 | 22 |
| GO:00068981 | Colorectum | MSS | receptor-mediated endocytosis | 69/3467 | 244/18723 | 1.18e-04 | 1.82e-03 | 69 |
| GO:00482681 | Colorectum | MSS | clathrin coat assembly | 10/3467 | 18/18723 | 4.76e-04 | 5.58e-03 | 10 |
| GO:0046394 | Colorectum | MSS | carboxylic acid biosynthetic process | 76/3467 | 314/18723 | 6.71e-03 | 4.38e-02 | 76 |
| GO:0016053 | Colorectum | MSS | organic acid biosynthetic process | 76/3467 | 316/18723 | 7.88e-03 | 4.84e-02 | 76 |
| GO:00463941 | Colorectum | MSI-H | carboxylic acid biosynthetic process | 36/1319 | 314/18723 | 2.68e-03 | 3.48e-02 | 36 |
| GO:00160531 | Colorectum | MSI-H | organic acid biosynthetic process | 36/1319 | 316/18723 | 2.98e-03 | 3.78e-02 | 36 |
| GO:00725832 | Colorectum | FAP | clathrin-dependent endocytosis | 21/2622 | 47/18723 | 3.45e-07 | 1.87e-05 | 21 |
| GO:00068982 | Colorectum | FAP | receptor-mediated endocytosis | 62/2622 | 244/18723 | 1.47e-06 | 6.39e-05 | 62 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05166211 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
| hsa0466810 | Esophagus | ESCC | TNF signaling pathway | 89/4205 | 114/8465 | 3.36e-10 | 4.01e-09 | 2.06e-09 | 89 |
| hsa040645 | Esophagus | ESCC | NF-kappa B signaling pathway | 67/4205 | 104/8465 | 1.62e-03 | 4.89e-03 | 2.50e-03 | 67 |
| hsa05166310 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
| hsa0466817 | Esophagus | ESCC | TNF signaling pathway | 89/4205 | 114/8465 | 3.36e-10 | 4.01e-09 | 2.06e-09 | 89 |
| hsa0406412 | Esophagus | ESCC | NF-kappa B signaling pathway | 67/4205 | 104/8465 | 1.62e-03 | 4.89e-03 | 2.50e-03 | 67 |
| 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 |
| LTA | TNFRSF1A | LTA_TNFRSF1A | LT | Cervix | ADJ |
| LTA | TNFRSF1B | LTA_TNFRSF1B | LT | Cervix | ADJ |
| LTA | TNFRSF14 | LTA_TNFRSF14 | LT | Cervix | ADJ |
| LTA | TNFRSF14 | LTA_TNFRSF14 | LT | Esophagus | ADJ |
| LTA | TNFRSF1A | LTA_TNFRSF1A | LT | Esophagus | ESCC |
| LTA | TNFRSF1B | LTA_TNFRSF1B | LT | Esophagus | ESCC |
| LTA | TNFRSF14 | LTA_TNFRSF14 | LT | Esophagus | ESCC |
| 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 |
| LTA | SNV | Missense_Mutation | c.250N>A | p.Asp84Asn | p.D84N | P01374 | protein_coding | tolerated(0.54) | probably_damaging(0.998) | TCGA-E2-A14P-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Targeted Molecular therapy | trastuzumab | SD | |
| LTA | deletion | Frame_Shift_Del | novel | c.371delN | p.Thr125ProfsTer67 | p.T125Pfs*67 | P01374 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| LTA | SNV | Missense_Mutation | c.610G>A | p.Ala204Thr | p.A204T | P01374 | protein_coding | deleterious(0) | possibly_damaging(0.729) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LTA | SNV | Missense_Mutation | novel | c.497N>T | p.Ser166Leu | p.S166L | P01374 | protein_coding | tolerated(0.06) | probably_damaging(0.998) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LTA | SNV | Missense_Mutation | c.295N>A | p.Leu99Ile | p.L99I | P01374 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| LTA | SNV | Missense_Mutation | novel | c.163N>T | p.His55Tyr | p.H55Y | P01374 | protein_coding | tolerated(0.25) | benign(0.001) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| LTA | SNV | Missense_Mutation | c.293C>A | p.Ser98Tyr | p.S98Y | P01374 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD | |
| LTA | SNV | Missense_Mutation | c.533N>T | p.Gly178Val | p.G178V | P01374 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-B5-A11N-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LTA | SNV | Missense_Mutation | rs377059622 | c.248N>T | p.Thr83Met | p.T83M | P01374 | protein_coding | tolerated(0.22) | possibly_damaging(0.702) | TCGA-D1-A0ZP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| LTA | SNV | Missense_Mutation | novel | c.98N>C | p.Gln33Pro | p.Q33P | P01374 | protein_coding | deleterious(0) | possibly_damaging(0.694) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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 |
| 4049 | LTA | DRUGGABLE GENOME | carbamazepine | CARBAMAZEPINE | 11294926 | |
| 4049 | LTA | DRUGGABLE GENOME | inhibitor | CHEMBL1743056 | PATECLIZUMAB | |
| 4049 | LTA | DRUGGABLE GENOME | inhibitor | CHEMBL1742988 | BAMINERCEPT | |
| 4049 | LTA | DRUGGABLE GENOME | Anti-LT alpha | |||
| 4049 | LTA | DRUGGABLE GENOME | BAMINERCEPT | BAMINERCEPT | ||
| 4049 | LTA | DRUGGABLE GENOME | abacavir | ABACAVIR |
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