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Gene: ORM1 |
Gene summary for ORM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ORM1 | Gene ID | 5004 |
| Gene name | orosomucoid 1 | |
| Gene Alias | AGP-A | |
| Cytomap | 9q32 | |
| Gene Type | protein-coding | GO ID | GO:0001816 | UniProtAcc | P02763 |
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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 |
| 5004 | ORM1 | NAFLD1 | Human | Liver | NAFLD | 1.42e-03 | 2.97e-02 | -0.04 |
| 5004 | ORM1 | HCC1_Meng | Human | Liver | HCC | 6.61e-81 | 6.37e-01 | 0.0246 |
| 5004 | ORM1 | HCC2_Meng | Human | Liver | HCC | 8.79e-13 | -6.21e-01 | 0.0107 |
| 5004 | ORM1 | cirrhotic1 | Human | Liver | Cirrhotic | 6.37e-06 | -3.19e-01 | 0.0202 |
| 5004 | ORM1 | cirrhotic2 | Human | Liver | Cirrhotic | 5.51e-06 | -2.71e-01 | 0.0201 |
| 5004 | ORM1 | cirrhotic3 | Human | Liver | Cirrhotic | 1.29e-03 | -3.08e-01 | 0.0215 |
| 5004 | ORM1 | HCC1 | Human | Liver | HCC | 1.06e-16 | 4.22e+00 | 0.5336 |
| 5004 | ORM1 | HCC2 | Human | Liver | HCC | 1.32e-19 | 6.98e+00 | 0.5341 |
| 5004 | ORM1 | Pt13.a | Human | Liver | HCC | 5.33e-82 | 1.11e+00 | 0.021 |
| 5004 | ORM1 | Pt13.b | Human | Liver | HCC | 1.13e-94 | 1.01e+00 | 0.0251 |
| 5004 | ORM1 | Pt13.c | Human | Liver | HCC | 1.26e-17 | 6.54e-01 | 0.0076 |
| 5004 | ORM1 | Pt14.a | Human | Liver | HCC | 5.82e-12 | 4.81e-01 | 0.0169 |
| 5004 | ORM1 | Pt14.b | Human | Liver | HCC | 7.27e-27 | 7.14e-01 | 0.018 |
| 5004 | ORM1 | Pt14.c | Human | Liver | HCC | 2.79e-08 | 7.65e-01 | 0.0054 |
| 5004 | ORM1 | Pt14.d | Human | Liver | HCC | 3.07e-29 | 5.90e-01 | 0.0143 |
| 5004 | ORM1 | S027 | Human | Liver | HCC | 1.03e-21 | 3.18e+00 | 0.2446 |
| 5004 | ORM1 | S028 | Human | Liver | HCC | 1.74e-42 | 2.74e+00 | 0.2503 |
| 5004 | ORM1 | S029 | Human | Liver | HCC | 1.51e-60 | 4.41e+00 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:0002526 | Liver | NAFLD | acute inflammatory response | 26/1882 | 112/18723 | 3.68e-05 | 9.23e-04 | 26 |
| GO:0006953 | Liver | NAFLD | acute-phase response | 13/1882 | 49/18723 | 8.43e-04 | 1.03e-02 | 13 |
| GO:00069531 | Liver | Cirrhotic | acute-phase response | 23/4634 | 49/18723 | 6.06e-04 | 4.67e-03 | 23 |
| GO:00025261 | Liver | Cirrhotic | acute inflammatory response | 40/4634 | 112/18723 | 6.16e-03 | 3.06e-02 | 40 |
| GO:00025262 | Liver | HCC | acute inflammatory response | 62/7958 | 112/18723 | 4.06e-03 | 1.77e-02 | 62 |
| GO:00069532 | Liver | HCC | acute-phase response | 30/7958 | 49/18723 | 6.31e-03 | 2.57e-02 | 30 |
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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 |
| ORM1 | SNV | Missense_Mutation | rs746492399 | c.143N>T | p.Ser48Leu | p.S48L | P02763 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AO-A12D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| ORM1 | SNV | Missense_Mutation | rs766337200 | c.242G>C | p.Arg81Thr | p.R81T | P02763 | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR |
| ORM1 | SNV | Missense_Mutation | rs139631990 | c.500N>A | p.Arg167His | p.R167H | P02763 | protein_coding | deleterious(0.02) | benign(0) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| ORM1 | SNV | Missense_Mutation | novel | c.19C>A | p.Leu7Ile | p.L7I | P02763 | protein_coding | deleterious(0.01) | possibly_damaging(0.906) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| ORM1 | insertion | In_Frame_Ins | novel | c.433_434insTAC | p.Tyr145delinsLeuHis | p.Y145delinsLH | P02763 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| ORM1 | SNV | Missense_Mutation | novel | c.388N>A | p.Leu130Ile | p.L130I | P02763 | protein_coding | tolerated(0.11) | possibly_damaging(0.564) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ORM1 | SNV | Missense_Mutation | c.462N>T | p.Glu154Asp | p.E154D | P02763 | protein_coding | deleterious(0.01) | benign(0.411) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ORM1 | SNV | Missense_Mutation | novel | c.287N>G | p.Tyr96Cys | p.Y96C | P02763 | protein_coding | tolerated(0.12) | probably_damaging(0.96) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| ORM1 | SNV | Missense_Mutation | novel | c.313N>G | p.Thr105Ala | p.T105A | P02763 | protein_coding | deleterious(0) | possibly_damaging(0.62) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| ORM1 | SNV | Missense_Mutation | c.254N>T | p.Thr85Ile | p.T85I | P02763 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-B5-A11N-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=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 |
| Page: 1 |
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