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Gene: LPCAT2 |
Gene summary for LPCAT2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LPCAT2 | Gene ID | 54947 |
| Gene name | lysophosphatidylcholine acyltransferase 2 | |
| Gene Alias | AGPAT11 | |
| Cytomap | 16q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0006629 | UniProtAcc | Q7L5N7 |
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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 |
| 54947 | LPCAT2 | P23T-E | Human | Esophagus | ESCC | 3.97e-15 | 2.19e-01 | 0.108 |
| 54947 | LPCAT2 | P24T-E | Human | Esophagus | ESCC | 5.87e-05 | 1.93e-01 | 0.1287 |
| 54947 | LPCAT2 | P26T-E | Human | Esophagus | ESCC | 5.74e-26 | 4.70e-01 | 0.1276 |
| 54947 | LPCAT2 | P27T-E | Human | Esophagus | ESCC | 1.94e-20 | 1.58e-01 | 0.1055 |
| 54947 | LPCAT2 | P28T-E | Human | Esophagus | ESCC | 5.47e-07 | 1.25e-01 | 0.1149 |
| 54947 | LPCAT2 | P30T-E | Human | Esophagus | ESCC | 8.84e-13 | 5.29e-01 | 0.137 |
| 54947 | LPCAT2 | P31T-E | Human | Esophagus | ESCC | 5.25e-33 | 5.90e-01 | 0.1251 |
| 54947 | LPCAT2 | P32T-E | Human | Esophagus | ESCC | 6.66e-41 | 7.85e-01 | 0.1666 |
| 54947 | LPCAT2 | P36T-E | Human | Esophagus | ESCC | 8.79e-11 | 3.97e-01 | 0.1187 |
| 54947 | LPCAT2 | P37T-E | Human | Esophagus | ESCC | 9.72e-19 | 4.38e-01 | 0.1371 |
| 54947 | LPCAT2 | P39T-E | Human | Esophagus | ESCC | 7.78e-12 | 8.94e-02 | 0.0894 |
| 54947 | LPCAT2 | P40T-E | Human | Esophagus | ESCC | 2.07e-06 | 1.88e-01 | 0.109 |
| 54947 | LPCAT2 | P42T-E | Human | Esophagus | ESCC | 3.08e-09 | 3.30e-01 | 0.1175 |
| 54947 | LPCAT2 | P44T-E | Human | Esophagus | ESCC | 3.56e-02 | 1.81e-01 | 0.1096 |
| 54947 | LPCAT2 | P47T-E | Human | Esophagus | ESCC | 9.85e-09 | 3.11e-02 | 0.1067 |
| 54947 | LPCAT2 | P48T-E | Human | Esophagus | ESCC | 3.14e-14 | 1.52e-01 | 0.0959 |
| 54947 | LPCAT2 | P49T-E | Human | Esophagus | ESCC | 2.52e-12 | 9.66e-01 | 0.1768 |
| 54947 | LPCAT2 | P52T-E | Human | Esophagus | ESCC | 8.75e-11 | 2.67e-01 | 0.1555 |
| 54947 | LPCAT2 | P54T-E | Human | Esophagus | ESCC | 3.66e-11 | 3.92e-01 | 0.0975 |
| 54947 | LPCAT2 | P56T-E | Human | Esophagus | ESCC | 5.15e-05 | 8.81e-01 | 0.1613 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:00066446 | Esophagus | ESCC | phospholipid metabolic process | 218/8552 | 383/18723 | 5.37e-06 | 5.59e-05 | 218 |
| GO:00066505 | Esophagus | ESCC | glycerophospholipid metabolic process | 174/8552 | 306/18723 | 4.92e-05 | 3.85e-04 | 174 |
| GO:00464864 | Esophagus | ESCC | glycerolipid metabolic process | 211/8552 | 392/18723 | 6.51e-04 | 3.46e-03 | 211 |
| GO:00086542 | Liver | HCC | phospholipid biosynthetic process | 150/7958 | 253/18723 | 4.77e-08 | 1.03e-06 | 150 |
| GO:00066444 | Liver | HCC | phospholipid metabolic process | 214/7958 | 383/18723 | 7.25e-08 | 1.48e-06 | 214 |
| GO:004648611 | Liver | HCC | glycerolipid metabolic process | 215/7958 | 392/18723 | 4.54e-07 | 7.49e-06 | 215 |
| GO:004501711 | Liver | HCC | glycerolipid biosynthetic process | 143/7958 | 252/18723 | 3.27e-06 | 4.31e-05 | 143 |
| GO:00066504 | Liver | HCC | glycerophospholipid metabolic process | 168/7958 | 306/18723 | 7.27e-06 | 8.62e-05 | 168 |
| GO:004647411 | Liver | HCC | glycerophospholipid biosynthetic process | 121/7958 | 211/18723 | 9.12e-06 | 1.06e-04 | 121 |
| GO:0036151 | Liver | HCC | phosphatidylcholine acyl-chain remodeling | 11/7958 | 14/18723 | 6.81e-03 | 2.73e-02 | 11 |
| GO:00086543 | Oral cavity | OSCC | phospholipid biosynthetic process | 130/7305 | 253/18723 | 3.96e-05 | 3.46e-04 | 130 |
| GO:00464743 | Oral cavity | OSCC | glycerophospholipid biosynthetic process | 102/7305 | 211/18723 | 3.50e-03 | 1.48e-02 | 102 |
| GO:00066445 | Oral cavity | OSCC | phospholipid metabolic process | 175/7305 | 383/18723 | 4.21e-03 | 1.71e-02 | 175 |
| GO:0008611 | Oral cavity | LP | ether lipid biosynthetic process | 7/4623 | 11/18723 | 7.01e-03 | 3.96e-02 | 7 |
| GO:0046504 | Oral cavity | LP | glycerol ether biosynthetic process | 7/4623 | 11/18723 | 7.01e-03 | 3.96e-02 | 7 |
| GO:0097384 | Oral cavity | LP | cellular lipid biosynthetic process | 7/4623 | 11/18723 | 7.01e-03 | 3.96e-02 | 7 |
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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 |
| LPCAT2 | SNV | Missense_Mutation | novel | c.514N>A | p.Val172Ile | p.V172I | Q7L5N7 | protein_coding | tolerated(1) | benign(0) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| LPCAT2 | SNV | Missense_Mutation | c.622T>A | p.Ser208Thr | p.S208T | Q7L5N7 | protein_coding | deleterious(0) | possibly_damaging(0.802) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| LPCAT2 | SNV | Missense_Mutation | c.930G>T | p.Met310Ile | p.M310I | Q7L5N7 | protein_coding | deleterious(0.01) | possibly_damaging(0.496) | TCGA-GM-A2DH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR | |
| LPCAT2 | insertion | Frame_Shift_Ins | novel | c.1292_1293insCTTCACTTCCACAAAG | p.Glu431AspfsTer13 | p.E431Dfs*13 | Q7L5N7 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LPCAT2 | deletion | Frame_Shift_Del | c.884delN | p.Asn297MetfsTer13 | p.N297Mfs*13 | Q7L5N7 | protein_coding | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| LPCAT2 | SNV | Missense_Mutation | rs569284862 | c.253G>A | p.Ala85Thr | p.A85T | Q7L5N7 | protein_coding | tolerated(0.41) | benign(0.001) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LPCAT2 | SNV | Missense_Mutation | rs762221312 | c.497N>A | p.Arg166Gln | p.R166Q | Q7L5N7 | protein_coding | deleterious(0.01) | possibly_damaging(0.497) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LPCAT2 | SNV | Missense_Mutation | novel | c.1188N>C | p.Leu396Phe | p.L396F | Q7L5N7 | protein_coding | deleterious(0.01) | possibly_damaging(0.729) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LPCAT2 | SNV | Missense_Mutation | rs762221312 | c.497G>A | p.Arg166Gln | p.R166Q | Q7L5N7 | protein_coding | deleterious(0.01) | possibly_damaging(0.497) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LPCAT2 | SNV | Missense_Mutation | novel | c.1055N>C | p.Lys352Thr | p.K352T | Q7L5N7 | protein_coding | deleterious(0.03) | probably_damaging(0.985) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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