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Gene: MALAT1 |
Gene summary for MALAT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MALAT1 | Gene ID | 378938 |
| Gene name | metastasis associated lung adenocarcinoma transcript 1 | |
| Gene Alias | HCN | |
| Cytomap | 11q13.1 | |
| Gene Type | ncRNA | GO ID | GO:0001666 | UniProtAcc | NA |
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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 |
| 378938 | MALAT1 | GSM4909281 | Human | Breast | IDC | 2.34e-04 | -1.44e-01 | 0.21 |
| 378938 | MALAT1 | GSM4909282 | Human | Breast | IDC | 1.04e-13 | -1.17e-01 | -0.0288 |
| 378938 | MALAT1 | GSM4909287 | Human | Breast | IDC | 4.57e-13 | -2.27e-01 | 0.2057 |
| 378938 | MALAT1 | GSM4909288 | Human | Breast | IDC | 3.24e-21 | -7.65e-01 | 0.0988 |
| 378938 | MALAT1 | GSM4909290 | Human | Breast | IDC | 8.00e-05 | -1.59e-01 | 0.2096 |
| 378938 | MALAT1 | GSM4909294 | Human | Breast | IDC | 4.83e-52 | -8.90e-01 | 0.2022 |
| 378938 | MALAT1 | GSM4909297 | Human | Breast | IDC | 1.77e-08 | 1.60e-01 | 0.1517 |
| 378938 | MALAT1 | GSM4909298 | Human | Breast | IDC | 1.53e-15 | 1.86e-01 | 0.1551 |
| 378938 | MALAT1 | GSM4909301 | Human | Breast | IDC | 6.60e-33 | 2.62e-01 | 0.1577 |
| 378938 | MALAT1 | GSM4909302 | Human | Breast | IDC | 1.25e-28 | 2.82e-01 | 0.1545 |
| 378938 | MALAT1 | GSM4909306 | Human | Breast | IDC | 1.85e-16 | 2.05e-01 | 0.1564 |
| 378938 | MALAT1 | GSM4909313 | Human | Breast | IDC | 3.65e-06 | -8.35e-02 | 0.0391 |
| 378938 | MALAT1 | GSM4909315 | Human | Breast | IDC | 6.74e-33 | -6.95e-01 | 0.21 |
| 378938 | MALAT1 | GSM4909316 | Human | Breast | IDC | 1.81e-32 | -1.14e+00 | 0.21 |
| 378938 | MALAT1 | GSM4909318 | Human | Breast | IDC | 4.80e-17 | -8.33e-01 | 0.2031 |
| 378938 | MALAT1 | GSM4909319 | Human | Breast | IDC | 3.54e-21 | 2.22e-01 | 0.1563 |
| 378938 | MALAT1 | GSM4909320 | Human | Breast | IDC | 3.31e-08 | 2.58e-01 | 0.1575 |
| 378938 | MALAT1 | ctrl6 | Human | Breast | Precancer | 6.29e-06 | 2.26e-01 | -0.0061 |
| 378938 | MALAT1 | brca1 | Human | Breast | Precancer | 2.13e-02 | -6.17e-02 | -0.0338 |
| 378938 | MALAT1 | brca2 | Human | Breast | Precancer | 1.20e-17 | 2.28e-01 | -0.024 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00362939 | Breast | Precancer | response to decreased oxygen levels | 53/1080 | 322/18723 | 4.09e-12 | 6.84e-10 | 53 |
| GO:00016669 | Breast | Precancer | response to hypoxia | 51/1080 | 307/18723 | 7.33e-12 | 1.11e-09 | 51 |
| GO:00704829 | Breast | Precancer | response to oxygen levels | 55/1080 | 347/18723 | 7.47e-12 | 1.11e-09 | 55 |
| GO:00362948 | Breast | Precancer | cellular response to decreased oxygen levels | 31/1080 | 161/18723 | 2.61e-09 | 2.11e-07 | 31 |
| GO:00714538 | Breast | Precancer | cellular response to oxygen levels | 32/1080 | 177/18723 | 7.32e-09 | 5.52e-07 | 32 |
| GO:00714565 | Breast | Precancer | cellular response to hypoxia | 29/1080 | 151/18723 | 8.98e-09 | 6.50e-07 | 29 |
| GO:007048214 | Breast | IDC | response to oxygen levels | 64/1434 | 347/18723 | 3.45e-11 | 5.57e-09 | 64 |
| GO:003629314 | Breast | IDC | response to decreased oxygen levels | 60/1434 | 322/18723 | 9.26e-11 | 1.25e-08 | 60 |
| GO:000166614 | Breast | IDC | response to hypoxia | 58/1434 | 307/18723 | 1.09e-10 | 1.38e-08 | 58 |
| GO:003629413 | Breast | IDC | cellular response to decreased oxygen levels | 34/1434 | 161/18723 | 4.73e-08 | 3.02e-06 | 34 |
| GO:007145613 | Breast | IDC | cellular response to hypoxia | 32/1434 | 151/18723 | 1.07e-07 | 6.26e-06 | 32 |
| GO:007145313 | Breast | IDC | cellular response to oxygen levels | 35/1434 | 177/18723 | 1.68e-07 | 9.10e-06 | 35 |
| GO:003629323 | Breast | DCIS | response to decreased oxygen levels | 60/1390 | 322/18723 | 2.64e-11 | 4.56e-09 | 60 |
| GO:007048223 | Breast | DCIS | response to oxygen levels | 63/1390 | 347/18723 | 2.66e-11 | 4.56e-09 | 63 |
| GO:000166623 | Breast | DCIS | response to hypoxia | 58/1390 | 307/18723 | 3.19e-11 | 5.16e-09 | 58 |
| GO:003629422 | Breast | DCIS | cellular response to decreased oxygen levels | 34/1390 | 161/18723 | 2.21e-08 | 1.49e-06 | 34 |
| GO:007145622 | Breast | DCIS | cellular response to hypoxia | 32/1390 | 151/18723 | 5.21e-08 | 3.17e-06 | 32 |
| GO:007145322 | Breast | DCIS | cellular response to oxygen levels | 35/1390 | 177/18723 | 7.89e-08 | 4.47e-06 | 35 |
| GO:000166610 | Cervix | CC | response to hypoxia | 61/2311 | 307/18723 | 1.04e-04 | 1.34e-03 | 61 |
| GO:007048210 | Cervix | CC | response to oxygen levels | 67/2311 | 347/18723 | 1.21e-04 | 1.51e-03 | 67 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 |
| Page: 1 |
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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 |
| 378938 | MALAT1 | NA | Cilobradine | CILOBRADINE | ||
| 378938 | MALAT1 | NA | ZD-7288 | CHEMBL2052019 | ||
| 378938 | MALAT1 | NA | SKL-NP | |||
| 378938 | MALAT1 | NA | Ivabradine | IVABRADINE | ||
| 378938 | MALAT1 | NA | Platinum compounds | 26729200 |
| Page: 1 |
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