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Gene: SLIT2 |
Gene summary for SLIT2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SLIT2 | Gene ID | 9353 |
| Gene name | slit guidance ligand 2 | |
| Gene Alias | SLIL3 | |
| Cytomap | 4p15.31 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | O94813 |
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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 |
| 9353 | SLIT2 | AEH-subject1 | Human | Endometrium | AEH | 6.24e-09 | 3.44e-01 | -0.3059 |
| 9353 | SLIT2 | AEH-subject2 | Human | Endometrium | AEH | 6.33e-04 | 3.41e-01 | -0.2525 |
| 9353 | SLIT2 | AEH-subject3 | Human | Endometrium | AEH | 2.92e-03 | 2.63e-01 | -0.2576 |
| 9353 | SLIT2 | AEH-subject4 | Human | Endometrium | AEH | 3.11e-08 | 4.72e-01 | -0.2657 |
| 9353 | SLIT2 | EEC-subject1 | Human | Endometrium | EEC | 8.84e-12 | 4.85e-01 | -0.2682 |
| 9353 | SLIT2 | EEC-subject2 | Human | Endometrium | EEC | 3.93e-54 | 1.10e+00 | -0.2607 |
| 9353 | SLIT2 | EEC-subject5 | Human | Endometrium | EEC | 2.56e-10 | 4.50e-01 | -0.249 |
| 9353 | SLIT2 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 7.52e-21 | 7.40e-01 | -0.1934 |
| 9353 | SLIT2 | TD9 | Human | Lung | IAC | 1.60e-04 | 1.02e+00 | 0.088 |
| 9353 | SLIT2 | RNA-P17T-P17T-2 | Human | Lung | IAC | 2.29e-03 | 5.78e-01 | 0.3371 |
| 9353 | SLIT2 | RNA-P17T-P17T-4 | Human | Lung | IAC | 4.12e-02 | 5.15e-01 | 0.343 |
| 9353 | SLIT2 | RNA-P17T-P17T-6 | Human | Lung | IAC | 4.45e-02 | 5.48e-01 | 0.3385 |
| 9353 | SLIT2 | RNA-P17T-P17T-8 | Human | Lung | IAC | 7.05e-06 | 6.53e-01 | 0.3329 |
| 9353 | SLIT2 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.89e-06 | 3.99e-01 | -0.2116 |
| 9353 | SLIT2 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 2.55e-03 | 3.88e-01 | -0.2119 |
| 9353 | SLIT2 | male-WTA | Human | Thyroid | PTC | 1.58e-25 | 3.00e-01 | 0.1037 |
| 9353 | SLIT2 | PTC01 | Human | Thyroid | PTC | 3.90e-06 | 1.75e-01 | 0.1899 |
| 9353 | SLIT2 | PTC04 | Human | Thyroid | PTC | 2.66e-06 | 6.46e-02 | 0.1927 |
| 9353 | SLIT2 | PTC05 | Human | Thyroid | PTC | 8.82e-03 | 2.74e-01 | 0.2065 |
| 9353 | SLIT2 | PTC06 | Human | Thyroid | PTC | 3.32e-19 | 6.12e-01 | 0.2057 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:006145812 | Lung | AIS | reproductive system development | 70/1849 | 427/18723 | 1.52e-05 | 5.50e-04 | 70 |
| GO:011005313 | Lung | AIS | regulation of actin filament organization | 50/1849 | 278/18723 | 2.13e-05 | 7.27e-04 | 50 |
| GO:004860811 | Lung | AIS | reproductive structure development | 69/1849 | 424/18723 | 2.23e-05 | 7.42e-04 | 69 |
| GO:012003213 | Lung | AIS | regulation of plasma membrane bounded cell projection assembly | 37/1849 | 186/18723 | 2.67e-05 | 8.60e-04 | 37 |
| GO:006049113 | Lung | AIS | regulation of cell projection assembly | 37/1849 | 188/18723 | 3.41e-05 | 1.05e-03 | 37 |
| GO:005149412 | Lung | AIS | negative regulation of cytoskeleton organization | 33/1849 | 163/18723 | 4.95e-05 | 1.43e-03 | 33 |
| GO:004325413 | Lung | AIS | regulation of protein-containing complex assembly | 68/1849 | 428/18723 | 5.51e-05 | 1.56e-03 | 68 |
| GO:000193313 | Lung | AIS | negative regulation of protein phosphorylation | 57/1849 | 342/18723 | 5.71e-05 | 1.60e-03 | 57 |
| GO:005125813 | Lung | AIS | protein polymerization | 51/1849 | 297/18723 | 6.29e-05 | 1.70e-03 | 51 |
| GO:005105811 | Lung | AIS | negative regulation of small GTPase mediated signal transduction | 16/1849 | 56/18723 | 6.89e-05 | 1.84e-03 | 16 |
| GO:190290413 | Lung | AIS | negative regulation of supramolecular fiber organization | 33/1849 | 167/18723 | 8.14e-05 | 2.03e-03 | 33 |
| GO:000166713 | Lung | AIS | ameboidal-type cell migration | 73/1849 | 475/18723 | 8.91e-05 | 2.20e-03 | 73 |
| GO:001097512 | Lung | AIS | regulation of neuron projection development | 69/1849 | 445/18723 | 1.05e-04 | 2.53e-03 | 69 |
| GO:003134612 | Lung | AIS | positive regulation of cell projection organization | 57/1849 | 353/18723 | 1.38e-04 | 3.05e-03 | 57 |
| GO:003227113 | Lung | AIS | regulation of protein polymerization | 41/1849 | 233/18723 | 1.85e-04 | 3.83e-03 | 41 |
| GO:00069291 | Lung | AIS | substrate-dependent cell migration | 9/1849 | 23/18723 | 1.98e-04 | 4.07e-03 | 9 |
| GO:000740911 | Lung | AIS | axonogenesis | 64/1849 | 418/18723 | 2.62e-04 | 5.04e-03 | 64 |
| GO:007207311 | Lung | AIS | kidney epithelium development | 27/1849 | 136/18723 | 3.21e-04 | 5.83e-03 | 27 |
| GO:009013211 | Lung | AIS | epithelium migration | 56/1849 | 360/18723 | 4.14e-04 | 7.14e-03 | 56 |
| GO:006156411 | Lung | AIS | axon development | 69/1849 | 467/18723 | 4.37e-04 | 7.41e-03 | 69 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0436010 | Endometrium | AEH | Axon guidance | 39/1197 | 182/8465 | 4.47e-03 | 2.46e-02 | 1.80e-02 | 39 |
| hsa0436013 | Endometrium | AEH | Axon guidance | 39/1197 | 182/8465 | 4.47e-03 | 2.46e-02 | 1.80e-02 | 39 |
| hsa0436022 | Endometrium | EEC | Axon guidance | 39/1237 | 182/8465 | 7.78e-03 | 3.66e-02 | 2.73e-02 | 39 |
| hsa0436032 | Endometrium | EEC | Axon guidance | 39/1237 | 182/8465 | 7.78e-03 | 3.66e-02 | 2.73e-02 | 39 |
| hsa043608 | Lung | IAC | Axon guidance | 34/1053 | 182/8465 | 9.31e-03 | 3.62e-02 | 2.41e-02 | 34 |
| hsa0436011 | Lung | IAC | Axon guidance | 34/1053 | 182/8465 | 9.31e-03 | 3.62e-02 | 2.41e-02 | 34 |
| hsa0436021 | Lung | AIS | Axon guidance | 34/961 | 182/8465 | 2.22e-03 | 1.37e-02 | 8.80e-03 | 34 |
| hsa0436031 | Lung | AIS | Axon guidance | 34/961 | 182/8465 | 2.22e-03 | 1.37e-02 | 8.80e-03 | 34 |
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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 |
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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. |
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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 |
| SLIT2 | SNV | Missense_Mutation | rs763158714 | c.1507N>T | p.Asp503Tyr | p.D503Y | O94813 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-A2-A4S1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SLIT2 | SNV | Missense_Mutation | novel | c.1115T>G | p.Phe372Cys | p.F372C | O94813 | protein_coding | tolerated(0.14) | possibly_damaging(0.763) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SLIT2 | SNV | Missense_Mutation | c.4003N>T | p.Pro1335Ser | p.P1335S | O94813 | protein_coding | tolerated(0.39) | benign(0.23) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SLIT2 | SNV | Missense_Mutation | novel | c.3353T>C | p.Val1118Ala | p.V1118A | O94813 | protein_coding | tolerated(0.34) | benign(0.009) | TCGA-AN-A0AL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SLIT2 | SNV | Missense_Mutation | rs749148075 | c.566N>T | p.Arg189Ile | p.R189I | O94813 | protein_coding | tolerated(0.39) | benign(0.216) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SLIT2 | SNV | Missense_Mutation | rs767628989 | c.673N>T | p.Arg225Cys | p.R225C | O94813 | protein_coding | deleterious(0) | probably_damaging(0.931) | TCGA-C8-A26W-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| SLIT2 | SNV | Missense_Mutation | c.1112N>C | p.Leu371Pro | p.L371P | O94813 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| SLIT2 | SNV | Missense_Mutation | c.1859G>T | p.Cys620Phe | p.C620F | O94813 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-E9-A24A-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| SLIT2 | SNV | Missense_Mutation | c.2668N>C | p.Gly890Arg | p.G890R | O94813 | protein_coding | tolerated(0.38) | benign(0.021) | TCGA-EW-A1IX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | femara | SD | |
| SLIT2 | SNV | Missense_Mutation | rs752006737 | c.3412N>A | p.Val1138Ile | p.V1138I | O94813 | protein_coding | tolerated(0.25) | benign(0.014) | TCGA-EW-A423-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 |
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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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