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Gene: LCAT |
Gene summary for LCAT |
Gene summary. |
Gene information | Species | Human | Gene symbol | LCAT | Gene ID | 3931 |
Gene name | lecithin-cholesterol acyltransferase | |
Gene Alias | LCAT | |
Cytomap | 16q22.1 | |
Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | A0A140VK24 |
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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 |
3931 | LCAT | male-WTA | Human | Thyroid | PTC | 2.77e-07 | 1.24e-01 | 0.1037 |
3931 | LCAT | PTC04 | Human | Thyroid | PTC | 5.43e-04 | 1.16e-01 | 0.1927 |
3931 | LCAT | PTC05 | Human | Thyroid | PTC | 1.59e-03 | 1.74e-01 | 0.2065 |
3931 | LCAT | PTC06 | Human | Thyroid | PTC | 5.58e-03 | 8.07e-02 | 0.2057 |
3931 | LCAT | PTC07 | Human | Thyroid | PTC | 1.28e-08 | 1.22e-01 | 0.2044 |
3931 | LCAT | ATC12 | Human | Thyroid | ATC | 5.43e-04 | 1.05e-01 | 0.34 |
3931 | LCAT | ATC13 | Human | Thyroid | ATC | 2.12e-37 | 5.56e-01 | 0.34 |
3931 | LCAT | ATC3 | Human | Thyroid | ATC | 1.02e-02 | 2.21e-01 | 0.338 |
3931 | LCAT | ATC4 | Human | Thyroid | ATC | 3.60e-04 | 1.34e-01 | 0.34 |
3931 | LCAT | ATC5 | Human | Thyroid | ATC | 4.37e-34 | 5.99e-01 | 0.34 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0043254113 | Thyroid | PTC | regulation of protein-containing complex assembly | 215/5968 | 428/18723 | 1.23e-15 | 9.09e-14 | 215 |
GO:0043254210 | Thyroid | ATC | regulation of protein-containing complex assembly | 225/6293 | 428/18723 | 2.72e-16 | 2.33e-14 | 225 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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 |
LCAT | SNV | Missense_Mutation | novel | c.1031N>T | p.Pro344Leu | p.P344L | P04180 | protein_coding | deleterious(0.02) | benign(0.007) | TCGA-DD-AACN-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
LCAT | SNV | Missense_Mutation | novel | c.34A>C | p.Thr12Pro | p.T12P | P04180 | protein_coding | deleterious_low_confidence(0.02) | benign(0) | TCGA-DD-AAVP-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
LCAT | insertion | Frame_Shift_Ins | novel | c.546_547insGG | p.Lys183GlyfsTer82 | p.K183Gfs*82 | P04180 | protein_coding | TCGA-XR-A8TG-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | ||
LCAT | SNV | Missense_Mutation | novel | c.693N>G | p.Ile231Met | p.I231M | P04180 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-44-2662-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Other, specify in notesGSK Mage Vaccine Study | rec | PD |
LCAT | SNV | Missense_Mutation | novel | c.945G>C | p.Trp315Cys | p.W315C | P04180 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-55-1592-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
LCAT | SNV | Missense_Mutation | novel | c.537N>C | p.Glu179Asp | p.E179D | P04180 | protein_coding | tolerated(0.34) | benign(0.287) | TCGA-86-8673-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
LCAT | SNV | Missense_Mutation | novel | c.1262C>T | p.Ala421Val | p.A421V | P04180 | protein_coding | deleterious_low_confidence(0.05) | benign(0.021) | TCGA-60-2719-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LCAT | SNV | Missense_Mutation | novel | c.856N>T | p.Asp286Tyr | p.D286Y | P04180 | protein_coding | deleterious(0) | possibly_damaging(0.776) | TCGA-85-8287-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LCAT | SNV | Missense_Mutation | novel | c.836N>G | p.Ser279Cys | p.S279C | P04180 | protein_coding | tolerated(0.12) | possibly_damaging(0.797) | TCGA-CR-6472-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | paclitaxel | SD |
LCAT | SNV | Missense_Mutation | novel | c.689N>C | p.Phe230Ser | p.F230S | P04180 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
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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 |
3931 | LCAT | ENZYME, TRANSPORTER, DRUGGABLE GENOME | MEDI6012 | RECOMBINANT HUMAN LECITHIN:CHOLESTEROL ACYLTRANSFERASE | 25657982 | |
3931 | LCAT | ENZYME, TRANSPORTER, DRUGGABLE GENOME | STREPTOZOTOCIN | STREPTOZOCIN | 18436977 | |
3931 | LCAT | ENZYME, TRANSPORTER, DRUGGABLE GENOME | TESTOSTERONE PROPIONATE | 3766045 | ||
3931 | LCAT | ENZYME, TRANSPORTER, DRUGGABLE GENOME | TESTOSTERONE | TESTOSTERONE | 3383436 | |
3931 | LCAT | ENZYME, TRANSPORTER, DRUGGABLE GENOME | PREDNISOLONE | PREDNISOLONE | 2314540 |
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