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Gene: SLITRK4 |
Gene summary for SLITRK4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SLITRK4 | Gene ID | 139065 |
| Gene name | SLIT and NTRK like family member 4 | |
| Gene Alias | SLITRK4 | |
| Cytomap | Xq27.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q8IW52 |
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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 |
| 139065 | SLITRK4 | PTC03 | Human | Thyroid | PTC | 1.79e-02 | 2.26e-01 | 0.1784 |
| 139065 | SLITRK4 | PTC05 | Human | Thyroid | PTC | 2.31e-02 | 1.34e-01 | 0.2065 |
| 139065 | SLITRK4 | ATC11 | Human | Thyroid | ATC | 1.60e-07 | 6.27e-01 | 0.3386 |
| 139065 | SLITRK4 | ATC3 | Human | Thyroid | ATC | 1.86e-15 | 8.59e-01 | 0.338 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:006156419 | Thyroid | PTC | axon development | 199/5968 | 467/18723 | 5.27e-07 | 8.53e-06 | 199 |
| GO:0034329111 | Thyroid | PTC | cell junction assembly | 180/5968 | 420/18723 | 1.17e-06 | 1.69e-05 | 180 |
| GO:000740918 | Thyroid | PTC | axonogenesis | 178/5968 | 418/18723 | 2.17e-06 | 2.91e-05 | 178 |
| GO:005196214 | Thyroid | PTC | positive regulation of nervous system development | 117/5968 | 272/18723 | 6.72e-05 | 5.89e-04 | 117 |
| GO:00519608 | Thyroid | PTC | regulation of nervous system development | 177/5968 | 443/18723 | 1.72e-04 | 1.32e-03 | 177 |
| GO:190188817 | Thyroid | PTC | regulation of cell junction assembly | 88/5968 | 204/18723 | 4.50e-04 | 2.97e-03 | 88 |
| GO:00508089 | Thyroid | PTC | synapse organization | 161/5968 | 426/18723 | 5.11e-03 | 2.36e-02 | 161 |
| GO:00508074 | Thyroid | PTC | regulation of synapse organization | 84/5968 | 211/18723 | 8.72e-03 | 3.64e-02 | 84 |
| GO:00508032 | Thyroid | PTC | regulation of synapse structure or activity | 86/5968 | 218/18723 | 1.05e-02 | 4.23e-02 | 86 |
| GO:006156423 | Thyroid | ATC | axon development | 220/6293 | 467/18723 | 6.85e-10 | 1.80e-08 | 220 |
| GO:000740919 | Thyroid | ATC | axonogenesis | 197/6293 | 418/18723 | 5.09e-09 | 1.13e-07 | 197 |
| GO:003432924 | Thyroid | ATC | cell junction assembly | 187/6293 | 420/18723 | 1.71e-06 | 2.08e-05 | 187 |
| GO:005196014 | Thyroid | ATC | regulation of nervous system development | 195/6293 | 443/18723 | 2.62e-06 | 3.06e-05 | 195 |
| GO:005196221 | Thyroid | ATC | positive regulation of nervous system development | 126/6293 | 272/18723 | 8.17e-06 | 8.27e-05 | 126 |
| GO:190188818 | Thyroid | ATC | regulation of cell junction assembly | 94/6293 | 204/18723 | 1.38e-04 | 9.65e-04 | 94 |
| GO:005080712 | Thyroid | ATC | regulation of synapse organization | 87/6293 | 211/18723 | 1.20e-02 | 4.27e-02 | 87 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| SLITRK4 | SNV | Missense_Mutation | c.881C>T | p.Thr294Ile | p.T294I | Q8IW52 | protein_coding | tolerated(0.24) | benign(0.065) | TCGA-A1-A0SK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| SLITRK4 | SNV | Missense_Mutation | novel | c.1960G>A | p.Glu654Lys | p.E654K | Q8IW52 | protein_coding | tolerated(0.13) | benign(0.034) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SLITRK4 | SNV | Missense_Mutation | c.611N>T | p.Arg204Leu | p.R204L | Q8IW52 | protein_coding | tolerated(0.12) | possibly_damaging(0.818) | TCGA-BH-A0BP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SLITRK4 | SNV | Missense_Mutation | novel | c.1126N>A | p.Pro376Thr | p.P376T | Q8IW52 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-BH-A5J0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SLITRK4 | SNV | Missense_Mutation | rs782728024 | c.770N>G | p.Asn257Ser | p.N257S | Q8IW52 | protein_coding | tolerated(1) | benign(0.014) | TCGA-D8-A1JJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD |
| SLITRK4 | SNV | Missense_Mutation | c.2502G>C | p.Leu834Phe | p.L834F | Q8IW52 | protein_coding | tolerated(1) | benign(0.031) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SLITRK4 | SNV | Missense_Mutation | c.1760C>T | p.Pro587Leu | p.P587L | Q8IW52 | protein_coding | tolerated(0.17) | benign(0.011) | TCGA-LL-A73Z-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| SLITRK4 | SNV | Missense_Mutation | novel | c.2233G>A | p.Glu745Lys | p.E745K | Q8IW52 | protein_coding | tolerated(0.67) | benign(0.428) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| SLITRK4 | SNV | Missense_Mutation | novel | c.1649N>A | p.Ser550Asn | p.S550N | Q8IW52 | protein_coding | tolerated(0.76) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SLITRK4 | SNV | Missense_Mutation | novel | c.1175N>C | p.Val392Ala | p.V392A | Q8IW52 | protein_coding | deleterious(0) | possibly_damaging(0.493) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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