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Gene: LPCAT1 |
Gene summary for LPCAT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LPCAT1 | Gene ID | 79888 |
| Gene name | lysophosphatidylcholine acyltransferase 1 | |
| Gene Alias | AGPAT10 | |
| Cytomap | 5p15.33 | |
| Gene Type | protein-coding | GO ID | GO:0001654 | UniProtAcc | Q8NF37 |
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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 |
| 79888 | LPCAT1 | LZE24T | Human | Esophagus | ESCC | 2.12e-05 | 1.01e-01 | 0.0596 |
| 79888 | LPCAT1 | P2T-E | Human | Esophagus | ESCC | 4.11e-15 | 2.70e-01 | 0.1177 |
| 79888 | LPCAT1 | P4T-E | Human | Esophagus | ESCC | 2.06e-09 | 1.93e-01 | 0.1323 |
| 79888 | LPCAT1 | P5T-E | Human | Esophagus | ESCC | 4.54e-14 | 3.12e-01 | 0.1327 |
| 79888 | LPCAT1 | P8T-E | Human | Esophagus | ESCC | 1.99e-05 | 1.30e-01 | 0.0889 |
| 79888 | LPCAT1 | P9T-E | Human | Esophagus | ESCC | 5.26e-07 | 1.85e-01 | 0.1131 |
| 79888 | LPCAT1 | P10T-E | Human | Esophagus | ESCC | 1.29e-33 | 6.37e-01 | 0.116 |
| 79888 | LPCAT1 | P11T-E | Human | Esophagus | ESCC | 1.57e-12 | 3.73e-01 | 0.1426 |
| 79888 | LPCAT1 | P12T-E | Human | Esophagus | ESCC | 9.27e-12 | 2.82e-01 | 0.1122 |
| 79888 | LPCAT1 | P15T-E | Human | Esophagus | ESCC | 4.00e-02 | 1.08e-01 | 0.1149 |
| 79888 | LPCAT1 | P16T-E | Human | Esophagus | ESCC | 3.41e-07 | 1.56e-01 | 0.1153 |
| 79888 | LPCAT1 | P17T-E | Human | Esophagus | ESCC | 3.87e-09 | 4.67e-01 | 0.1278 |
| 79888 | LPCAT1 | P19T-E | Human | Esophagus | ESCC | 3.94e-02 | 3.20e-01 | 0.1662 |
| 79888 | LPCAT1 | P20T-E | Human | Esophagus | ESCC | 2.85e-11 | 2.07e-01 | 0.1124 |
| 79888 | LPCAT1 | P21T-E | Human | Esophagus | ESCC | 7.09e-20 | 4.69e-01 | 0.1617 |
| 79888 | LPCAT1 | P22T-E | Human | Esophagus | ESCC | 5.45e-11 | 2.24e-01 | 0.1236 |
| 79888 | LPCAT1 | P24T-E | Human | Esophagus | ESCC | 4.47e-04 | 1.20e-01 | 0.1287 |
| 79888 | LPCAT1 | P26T-E | Human | Esophagus | ESCC | 6.28e-04 | 1.53e-01 | 0.1276 |
| 79888 | LPCAT1 | P27T-E | Human | Esophagus | ESCC | 1.24e-03 | 7.83e-02 | 0.1055 |
| 79888 | LPCAT1 | P28T-E | Human | Esophagus | ESCC | 4.94e-09 | 2.08e-01 | 0.1149 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:0150172 | Lung | IAC | regulation of phosphatidylcholine metabolic process | 5/2061 | 10/18723 | 2.52e-03 | 2.34e-02 | 5 |
| GO:00602497 | Lung | IAC | anatomical structure homeostasis | 51/2061 | 314/18723 | 2.91e-03 | 2.61e-02 | 51 |
| GO:004217613 | Lung | AIS | regulation of protein catabolic process | 92/1849 | 391/18723 | 1.34e-15 | 3.91e-12 | 92 |
| GO:000989613 | Lung | AIS | positive regulation of catabolic process | 103/1849 | 492/18723 | 9.59e-14 | 1.86e-10 | 103 |
| GO:004573213 | Lung | AIS | positive regulation of protein catabolic process | 60/1849 | 231/18723 | 1.47e-12 | 2.14e-09 | 60 |
| GO:00488751 | Lung | AIS | chemical homeostasis within a tissue | 9/1849 | 14/18723 | 1.11e-06 | 7.51e-05 | 9 |
| GO:004593613 | Lung | AIS | negative regulation of phosphate metabolic process | 75/1849 | 441/18723 | 1.93e-06 | 1.12e-04 | 75 |
| GO:001056313 | Lung | AIS | negative regulation of phosphorus metabolic process | 75/1849 | 442/18723 | 2.11e-06 | 1.20e-04 | 75 |
| GO:00431291 | Lung | AIS | surfactant homeostasis | 8/1849 | 12/18723 | 3.07e-06 | 1.64e-04 | 8 |
| GO:01501721 | Lung | AIS | regulation of phosphatidylcholine metabolic process | 5/1849 | 10/18723 | 1.54e-03 | 1.82e-02 | 5 |
| GO:000189412 | Lung | AIS | tissue homeostasis | 41/1849 | 268/18723 | 3.13e-03 | 3.01e-02 | 41 |
| GO:00464701 | Lung | AIS | phosphatidylcholine metabolic process | 15/1849 | 74/18723 | 5.25e-03 | 4.49e-02 | 15 |
| GO:00488752 | Lung | AAH | chemical homeostasis within a tissue | 7/613 | 14/18723 | 1.10e-07 | 6.77e-05 | 7 |
| GO:00431292 | Lung | AAH | surfactant homeostasis | 6/613 | 12/18723 | 9.39e-07 | 3.07e-04 | 6 |
| GO:000989623 | Lung | AAH | positive regulation of catabolic process | 34/613 | 492/18723 | 3.70e-05 | 4.47e-03 | 34 |
| GO:004217623 | Lung | AAH | regulation of protein catabolic process | 29/613 | 391/18723 | 3.92e-05 | 4.60e-03 | 29 |
| GO:004573223 | Lung | AAH | positive regulation of protein catabolic process | 20/613 | 231/18723 | 7.76e-05 | 6.21e-03 | 20 |
| GO:01501722 | Lung | AAH | regulation of phosphatidylcholine metabolic process | 4/613 | 10/18723 | 2.04e-04 | 1.13e-02 | 4 |
| GO:000189422 | Lung | AAH | tissue homeostasis | 21/613 | 268/18723 | 2.12e-04 | 1.16e-02 | 21 |
| GO:006024912 | Lung | AAH | anatomical structure homeostasis | 23/613 | 314/18723 | 2.89e-04 | 1.45e-02 | 23 |
| Page: 1 2 3 4 5 |
| 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 |
| LPCAT1 | SNV | Missense_Mutation | novel | c.1351N>T | p.Val451Leu | p.V451L | Q8NF37 | protein_coding | tolerated(0.1) | benign(0.031) | TCGA-B6-A0I1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| LPCAT1 | SNV | Missense_Mutation | c.1382N>A | p.Arg461Gln | p.R461Q | Q8NF37 | protein_coding | tolerated(0.52) | benign(0.003) | TCGA-B6-A0WY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| LPCAT1 | SNV | Missense_Mutation | c.1600N>C | p.Asp534His | p.D534H | Q8NF37 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.781) | TCGA-BH-A0BP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LPCAT1 | SNV | Missense_Mutation | c.1588C>T | p.Arg530Cys | p.R530C | Q8NF37 | protein_coding | tolerated_low_confidence(0.26) | benign(0) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| LPCAT1 | SNV | Missense_Mutation | novel | c.999A>T | p.Glu333Asp | p.E333D | Q8NF37 | protein_coding | deleterious(0) | possibly_damaging(0.831) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LPCAT1 | SNV | Missense_Mutation | novel | c.559G>T | p.Val187Leu | p.V187L | Q8NF37 | protein_coding | deleterious(0.04) | possibly_damaging(0.771) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LPCAT1 | SNV | Missense_Mutation | c.814N>C | p.Glu272Gln | p.E272Q | Q8NF37 | protein_coding | deleterious(0.02) | probably_damaging(0.91) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| LPCAT1 | SNV | Missense_Mutation | rs747860604 | c.358N>T | p.Arg120Trp | p.R120W | Q8NF37 | protein_coding | deleterious(0) | probably_damaging(0.93) | TCGA-4T-AA8H-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LPCAT1 | SNV | Missense_Mutation | novel | c.655A>G | p.Thr219Ala | p.T219A | Q8NF37 | protein_coding | deleterious(0.02) | benign(0.081) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| LPCAT1 | SNV | Missense_Mutation | c.392N>T | p.Thr131Met | p.T131M | Q8NF37 | protein_coding | deleterious(0.01) | possibly_damaging(0.829) | TCGA-AA-3819-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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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