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Gene: LST1 |
Gene summary for LST1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LST1 | Gene ID | 7940 |
| Gene name | leukocyte specific transcript 1 | |
| Gene Alias | B144 | |
| Cytomap | 6p21.33 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O00453 |
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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 |
| 7940 | LST1 | CCI_1 | Human | Cervix | CC | 2.41e-04 | -5.22e-01 | 0.528 |
| 7940 | LST1 | CCI_2 | Human | Cervix | CC | 7.57e-04 | -5.22e-01 | 0.5249 |
| 7940 | LST1 | CCI_3 | Human | Cervix | CC | 2.34e-04 | -5.07e-01 | 0.516 |
| 7940 | LST1 | CCII_1 | Human | Cervix | CC | 2.76e-07 | -5.11e-01 | 0.3249 |
| 7940 | LST1 | Tumor | Human | Cervix | CC | 3.60e-17 | -5.17e-01 | 0.1241 |
| 7940 | LST1 | sample1 | Human | Cervix | CC | 3.43e-03 | -4.57e-01 | 0.0959 |
| 7940 | LST1 | sample3 | Human | Cervix | CC | 3.12e-19 | -5.22e-01 | 0.1387 |
| 7940 | LST1 | H2 | Human | Cervix | HSIL_HPV | 4.37e-17 | -5.10e-01 | 0.0632 |
| 7940 | LST1 | T1 | Human | Cervix | CC | 7.83e-13 | -4.93e-01 | 0.0918 |
| 7940 | LST1 | T2 | Human | Cervix | CC | 1.52e-03 | -5.22e-01 | 0.0709 |
| 7940 | LST1 | T3 | Human | Cervix | CC | 3.12e-19 | -5.19e-01 | 0.1389 |
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| 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 |
| ∗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:002260410 | Cervix | CC | regulation of cell morphogenesis | 84/2311 | 309/18723 | 1.00e-12 | 4.29e-10 | 84 |
| GO:00026837 | Cervix | CC | negative regulation of immune system process | 94/2311 | 434/18723 | 2.63e-08 | 1.87e-06 | 94 |
| GO:00163587 | Cervix | CC | dendrite development | 58/2311 | 243/18723 | 4.52e-07 | 1.76e-05 | 58 |
| GO:00706637 | Cervix | CC | regulation of leukocyte proliferation | 55/2311 | 245/18723 | 6.51e-06 | 1.56e-04 | 55 |
| GO:00506705 | Cervix | CC | regulation of lymphocyte proliferation | 51/2311 | 225/18723 | 1.05e-05 | 2.32e-04 | 51 |
| GO:0051250 | Cervix | CC | negative regulation of lymphocyte activation | 39/2311 | 157/18723 | 1.23e-05 | 2.57e-04 | 39 |
| GO:00329444 | Cervix | CC | regulation of mononuclear cell proliferation | 51/2311 | 227/18723 | 1.36e-05 | 2.73e-04 | 51 |
| GO:00083608 | Cervix | CC | regulation of cell shape | 38/2311 | 154/18723 | 1.86e-05 | 3.46e-04 | 38 |
| GO:00706617 | Cervix | CC | leukocyte proliferation | 65/2311 | 318/18723 | 2.56e-05 | 4.32e-04 | 65 |
| GO:0002695 | Cervix | CC | negative regulation of leukocyte activation | 43/2311 | 187/18723 | 3.47e-05 | 5.60e-04 | 43 |
| GO:00466516 | Cervix | CC | lymphocyte proliferation | 59/2311 | 288/18723 | 5.53e-05 | 8.10e-04 | 59 |
| GO:00329435 | Cervix | CC | mononuclear cell proliferation | 59/2311 | 291/18723 | 7.51e-05 | 1.03e-03 | 59 |
| GO:0050866 | Cervix | CC | negative regulation of cell activation | 44/2311 | 210/18723 | 2.76e-04 | 3.02e-03 | 44 |
| GO:0070664 | Cervix | CC | negative regulation of leukocyte proliferation | 21/2311 | 90/18723 | 2.71e-03 | 1.85e-02 | 21 |
| GO:0050672 | Cervix | CC | negative regulation of lymphocyte proliferation | 19/2311 | 83/18723 | 5.25e-03 | 3.08e-02 | 19 |
| GO:0032945 | Cervix | CC | negative regulation of mononuclear cell proliferation | 19/2311 | 84/18723 | 6.02e-03 | 3.43e-02 | 19 |
| GO:000268312 | Cervix | HSIL_HPV | negative regulation of immune system process | 39/737 | 434/18723 | 1.51e-06 | 6.60e-05 | 39 |
| GO:005067012 | Cervix | HSIL_HPV | regulation of lymphocyte proliferation | 24/737 | 225/18723 | 9.64e-06 | 3.32e-04 | 24 |
| GO:003294412 | Cervix | HSIL_HPV | regulation of mononuclear cell proliferation | 24/737 | 227/18723 | 1.12e-05 | 3.72e-04 | 24 |
| GO:007066312 | Cervix | HSIL_HPV | regulation of leukocyte proliferation | 25/737 | 245/18723 | 1.37e-05 | 4.32e-04 | 25 |
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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 |
| LST1 | SNV | Missense_Mutation | novel | c.267N>T | p.Glu89Asp | p.E89D | O00453 | protein_coding | tolerated(0.07) | possibly_damaging(0.722) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LST1 | SNV | Missense_Mutation | rs550132083 | c.10C>T | p.Arg4Trp | p.R4W | O00453 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| LST1 | SNV | Missense_Mutation | novel | c.248A>G | p.Asp83Gly | p.D83G | O00453 | protein_coding | tolerated(0.16) | benign(0.265) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
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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 |
| 7940 | LST1 | NA | abacavir | ABACAVIR |
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