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Gene: LINC01004 |
Gene summary for LINC01004 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LINC01004 | Gene ID | 100216546 |
| Gene name | long intergenic non-protein coding RNA 1004 | |
| Gene Alias | LINC01004 | |
| Cytomap | 7q22.3 | |
| Gene Type | ncRNA | GO ID | GO:0005575 | 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 |
| 100216546 | LINC01004 | CCI_1 | Human | Cervix | CC | 5.92e-15 | 8.93e-01 | 0.528 |
| 100216546 | LINC01004 | CCI_2 | Human | Cervix | CC | 1.84e-19 | 8.48e-01 | 0.5249 |
| 100216546 | LINC01004 | CCI_3 | Human | Cervix | CC | 2.29e-28 | 9.68e-01 | 0.516 |
| 100216546 | LINC01004 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.92e-03 | -2.64e-01 | 0.0155 |
| 100216546 | LINC01004 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.08e-16 | 8.49e-01 | -0.1954 |
| 100216546 | LINC01004 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.01e-06 | -3.35e-01 | 0.294 |
| 100216546 | LINC01004 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.81e-04 | -2.95e-01 | 0.3859 |
| 100216546 | LINC01004 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.13e-08 | -3.98e-01 | 0.3005 |
| 100216546 | LINC01004 | A001-C-207 | Human | Colorectum | FAP | 4.38e-08 | -4.51e-01 | 0.1278 |
| 100216546 | LINC01004 | A015-C-203 | Human | Colorectum | FAP | 6.74e-33 | -5.16e-01 | -0.1294 |
| 100216546 | LINC01004 | A015-C-204 | Human | Colorectum | FAP | 1.33e-10 | -5.02e-01 | -0.0228 |
| 100216546 | LINC01004 | A014-C-040 | Human | Colorectum | FAP | 2.78e-04 | -3.85e-01 | -0.1184 |
| 100216546 | LINC01004 | A002-C-201 | Human | Colorectum | FAP | 1.02e-12 | -4.30e-01 | 0.0324 |
| 100216546 | LINC01004 | A002-C-203 | Human | Colorectum | FAP | 1.65e-05 | -8.04e-02 | 0.2786 |
| 100216546 | LINC01004 | A001-C-119 | Human | Colorectum | FAP | 2.46e-07 | -4.35e-01 | -0.1557 |
| 100216546 | LINC01004 | A001-C-108 | Human | Colorectum | FAP | 1.60e-20 | -4.73e-01 | -0.0272 |
| 100216546 | LINC01004 | A002-C-205 | Human | Colorectum | FAP | 1.59e-20 | -4.50e-01 | -0.1236 |
| 100216546 | LINC01004 | A001-C-104 | Human | Colorectum | FAP | 1.23e-09 | -4.76e-01 | 0.0184 |
| 100216546 | LINC01004 | A015-C-005 | Human | Colorectum | FAP | 6.44e-08 | -4.45e-01 | -0.0336 |
| 100216546 | LINC01004 | A015-C-006 | Human | Colorectum | FAP | 2.81e-18 | -6.40e-01 | -0.0994 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 |
| ∗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 |
| Page: 1 |
| 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 |
| Page: 1 |
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