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Gene: ORMDL2 |
Gene summary for ORMDL2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ORMDL2 | Gene ID | 29095 |
| Gene name | ORMDL sphingolipid biosynthesis regulator 2 | |
| Gene Alias | HSPC160 | |
| Cytomap | 12q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006629 | UniProtAcc | Q53FV1 |
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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 |
| 29095 | ORMDL2 | LZE2T | Human | Esophagus | ESCC | 5.56e-04 | 7.64e-01 | 0.082 |
| 29095 | ORMDL2 | LZE4T | Human | Esophagus | ESCC | 1.51e-12 | 3.86e-01 | 0.0811 |
| 29095 | ORMDL2 | LZE7T | Human | Esophagus | ESCC | 5.44e-05 | 4.63e-01 | 0.0667 |
| 29095 | ORMDL2 | LZE8T | Human | Esophagus | ESCC | 2.07e-05 | 1.78e-01 | 0.067 |
| 29095 | ORMDL2 | LZE20T | Human | Esophagus | ESCC | 1.32e-11 | 5.45e-01 | 0.0662 |
| 29095 | ORMDL2 | LZE24T | Human | Esophagus | ESCC | 1.24e-28 | 9.29e-01 | 0.0596 |
| 29095 | ORMDL2 | LZE22D3 | Human | Esophagus | HGIN | 1.52e-02 | 5.87e-01 | 0.0653 |
| 29095 | ORMDL2 | LZE6T | Human | Esophagus | ESCC | 7.97e-08 | 6.44e-01 | 0.0845 |
| 29095 | ORMDL2 | P1T-E | Human | Esophagus | ESCC | 4.36e-07 | 7.22e-01 | 0.0875 |
| 29095 | ORMDL2 | P2T-E | Human | Esophagus | ESCC | 3.65e-35 | 7.99e-01 | 0.1177 |
| 29095 | ORMDL2 | P4T-E | Human | Esophagus | ESCC | 2.14e-46 | 1.30e+00 | 0.1323 |
| 29095 | ORMDL2 | P5T-E | Human | Esophagus | ESCC | 9.07e-79 | 1.70e+00 | 0.1327 |
| 29095 | ORMDL2 | P8T-E | Human | Esophagus | ESCC | 1.03e-24 | 7.42e-01 | 0.0889 |
| 29095 | ORMDL2 | P9T-E | Human | Esophagus | ESCC | 4.17e-22 | 6.41e-01 | 0.1131 |
| 29095 | ORMDL2 | P10T-E | Human | Esophagus | ESCC | 1.71e-19 | 4.77e-01 | 0.116 |
| 29095 | ORMDL2 | P11T-E | Human | Esophagus | ESCC | 2.42e-11 | 6.79e-01 | 0.1426 |
| 29095 | ORMDL2 | P12T-E | Human | Esophagus | ESCC | 2.19e-26 | 6.14e-01 | 0.1122 |
| 29095 | ORMDL2 | P15T-E | Human | Esophagus | ESCC | 1.27e-36 | 8.02e-01 | 0.1149 |
| 29095 | ORMDL2 | P16T-E | Human | Esophagus | ESCC | 4.00e-18 | 4.31e-01 | 0.1153 |
| 29095 | ORMDL2 | P17T-E | Human | Esophagus | ESCC | 3.78e-12 | 9.26e-01 | 0.1278 |
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| 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:00342496 | Esophagus | HGIN | negative regulation of cellular amide metabolic process | 66/2587 | 273/18723 | 2.74e-06 | 9.60e-05 | 66 |
| GO:00066433 | Esophagus | ESCC | membrane lipid metabolic process | 130/8552 | 203/18723 | 9.29e-08 | 1.54e-06 | 130 |
| GO:00464673 | Esophagus | ESCC | membrane lipid biosynthetic process | 91/8552 | 142/18723 | 7.19e-06 | 7.19e-05 | 91 |
| GO:00066652 | Esophagus | ESCC | sphingolipid metabolic process | 96/8552 | 155/18723 | 3.21e-05 | 2.66e-04 | 96 |
| GO:00301481 | Esophagus | ESCC | sphingolipid biosynthetic process | 62/8552 | 103/18723 | 2.10e-03 | 9.38e-03 | 62 |
| GO:00066721 | Esophagus | ESCC | ceramide metabolic process | 61/8552 | 102/18723 | 2.82e-03 | 1.19e-02 | 61 |
| GO:0046513 | Esophagus | ESCC | ceramide biosynthetic process | 40/8552 | 65/18723 | 7.25e-03 | 2.63e-02 | 40 |
| GO:003424914 | Esophagus | ESCC | negative regulation of cellular amide metabolic process | 144/8552 | 273/18723 | 1.08e-02 | 3.67e-02 | 144 |
| GO:00192168 | Esophagus | ESCC | regulation of lipid metabolic process | 172/8552 | 331/18723 | 1.20e-02 | 4.02e-02 | 172 |
| GO:005508811 | Liver | Cirrhotic | lipid homeostasis | 74/4634 | 167/18723 | 2.46e-08 | 8.51e-07 | 74 |
| GO:001921611 | Liver | Cirrhotic | regulation of lipid metabolic process | 119/4634 | 331/18723 | 3.05e-06 | 5.39e-05 | 119 |
| GO:003424911 | Liver | Cirrhotic | negative regulation of cellular amide metabolic process | 100/4634 | 273/18723 | 7.34e-06 | 1.13e-04 | 100 |
| GO:004689011 | Liver | Cirrhotic | regulation of lipid biosynthetic process | 67/4634 | 171/18723 | 2.00e-05 | 2.65e-04 | 67 |
| GO:0006643 | Liver | Cirrhotic | membrane lipid metabolic process | 69/4634 | 203/18723 | 1.89e-03 | 1.19e-02 | 69 |
| GO:00550882 | Liver | HCC | lipid homeostasis | 103/7958 | 167/18723 | 4.27e-07 | 7.18e-06 | 103 |
| GO:00192162 | Liver | HCC | regulation of lipid metabolic process | 181/7958 | 331/18723 | 4.58e-06 | 5.79e-05 | 181 |
| GO:00066431 | Liver | HCC | membrane lipid metabolic process | 115/7958 | 203/18723 | 3.17e-05 | 3.22e-04 | 115 |
| GO:00468902 | Liver | HCC | regulation of lipid biosynthetic process | 96/7958 | 171/18723 | 2.14e-04 | 1.63e-03 | 96 |
| GO:003424921 | Liver | HCC | negative regulation of cellular amide metabolic process | 144/7958 | 273/18723 | 3.80e-04 | 2.61e-03 | 144 |
| GO:0006665 | Liver | HCC | sphingolipid metabolic process | 85/7958 | 155/18723 | 1.27e-03 | 6.92e-03 | 85 |
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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 |
| ORMDL2 | insertion | Nonsense_Mutation | novel | c.373_374insCAAAGTAAATGCTGTTGATATAGCTGGAATAGT | p.Leu125delinsProLysTerMetLeuLeuIleTerLeuGluTerPhe | p.L125delinsPK*MLLI*LE*F | Q53FV1 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| ORMDL2 | SNV | Missense_Mutation | rs766915849 | c.365N>T | p.Ala122Val | p.A122V | Q53FV1 | protein_coding | tolerated(0.7) | benign(0.003) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| ORMDL2 | SNV | Missense_Mutation | novel | c.193N>A | p.His65Asn | p.H65N | Q53FV1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| ORMDL2 | SNV | Missense_Mutation | c.427C>T | p.His143Tyr | p.H143Y | Q53FV1 | protein_coding | tolerated(0.12) | benign(0.381) | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| ORMDL2 | SNV | Missense_Mutation | c.32N>G | p.Asn11Ser | p.N11S | Q53FV1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EI-6507-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| ORMDL2 | SNV | Missense_Mutation | rs766915849 | c.365C>T | p.Ala122Val | p.A122V | Q53FV1 | protein_coding | tolerated(0.7) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| ORMDL2 | SNV | Missense_Mutation | novel | c.270N>A | p.Asp90Glu | p.D90E | Q53FV1 | protein_coding | deleterious(0) | possibly_damaging(0.883) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ORMDL2 | SNV | Missense_Mutation | c.189C>A | p.Phe63Leu | p.F63L | Q53FV1 | protein_coding | tolerated(0.4) | benign(0.003) | TCGA-55-7570-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| ORMDL2 | SNV | Missense_Mutation | c.421N>G | p.Gln141Glu | p.Q141E | Q53FV1 | protein_coding | deleterious(0.04) | benign(0.034) | TCGA-37-3783-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| ORMDL2 | deletion | Frame_Shift_Del | novel | c.145delN | p.Trp49GlyfsTer3 | p.W49Gfs*3 | Q53FV1 | protein_coding | TCGA-UF-A71E-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
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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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