Visualizing the structure of RNA-seq expression data using grade of membership models
-PCA, t-SNE, Hierarchical clustering 활용
The expression landscape of the solute carrier family (SLC) in brain tumors.
The expression landscape of the solute carrier family (SLC) in hepatocellular carcinoma.
volcano 활용 - https://www.biostars.org/p/268514/
clusterprofiler - https://www.biorxiv.org/content/biorxiv/early/2018/01/31/256784.full.pdf
뇌그림 참고 - https://arxiv.org/pdf/1706.06088.pdf
Correlation Figure 5 참고 - https://www.biorxiv.org/content/10.1101/237446v1.full
Matrix plot Figure 1 참고 - https://www.biorxiv.org/content/10.1101/236869v1.full
Figure 4참고 - https://www.nature.com/articles/s41588-018-0336-0
Matrix dot plot 참고 - https://www.cell.com/current-biology/pdf/S0960-9822(18)30225-2.pdf
SplitDotPlotGG - https://github.com/satijalab/seurat/issues/681
뇌, dotplot응용 참고 - https://www.biorxiv.org/content/10.1101/384479v3.full
(Review) SLC classification
1. Classification Systems of Secondary Active Transporters.
Trends Pharmacol Sci. 2017 Mar;38(3):305-315. doi: 10.1016/j.tips.2016.11.008. Epub 2016 Dec 9. https://www.ncbi.nlm.nih.gov/pubmed/27939446
Citations 53
(Review) SLC in cancers
1. Solute carrier transporters: potential targets for digestive system neoplasms.
Cancer Manag Res. 2018 Jan 24;10:153-166. doi: 10.2147/CMAR.S152951. eCollection 2018. https://www.ncbi.nlm.nih.gov/pubmed/29416375
Citations 5
2. Harnessing Solute Carrier Transporters for Precision Oncology.
Molecules. 2017 Apr; 22(4): 539. Published online 2017 Mar 28. doi: 10.3390/molecules22040539 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570559/
Citations 7
3. Emerging roles of metal solute carriers in cancer mechanisms and treatment.
Biopharm Drug Dispos. 2014 Nov;35(8):450-62. doi: 10.1002/bdd.1903. Epub 2014 Sep 5.
https://www.ncbi.nlm.nih.gov/pubmed/24889085
Citations 9
4. Role of solute carriers in response to anticancer drugs.
Mol Cell Ther. 2014 May 27;2:15. doi: 10.1186/2052-8426-2-15. eCollection 2014.
https://www.ncbi.nlm.nih.gov/pubmed/26056583
Citations 53
5. Role of solute carrier transporters in pancreatic cancer: a review.
Pharmacogenomics. 2014 Jun;15(8):1133-45. doi: 10.2217/pgs.14.80.
https://www.ncbi.nlm.nih.gov/pubmed/25084206
Citations 13
6. Solute carriers (SLCs) in cancer.
Mol Aspects Med. 2013 Apr-Jun;34(2-3):719-34. doi: 10.1016/j.mam.2012.12.007.
https://www.ncbi.nlm.nih.gov/pubmed/23506905
Citations 38
7. Contribution of tumoral and host solute carriers to clinical drug response.
Drug Resist Updat. 2012 Feb-Apr;15(1-2):5-20. doi: 10.1016/j.drup.2012.01.009. Epub 2012 Mar 28. https://www.ncbi.nlm.nih.gov/pubmed/22459901
Citations 21
8. Comparison of human solute carriers.
Protein Science. 22 February 2010. https://doi.org/10.1002/pro.320
Citation 93
9. Solute carriers as drug targets: current use, clinical trials and prospective.
Molecular Aspects of Medicine. 2013. https://doi.org/10.1016/j.mam.2012.07.015
Citation 58
(Review) SLC in BBB
1. Solute Carriers in the Blood-Brain Barier: Safety in Abundance.
Neurochem Res. 2017 Mar;42(3):795-809. doi: 10.1007/s11064-016-2030-x. Epub 2016 Aug 9. https://www.ncbi.nlm.nih.gov/pubmed/27503090
Citations 16
2. Efflux proteins at the blood-brain barrier: review and bioinformatics analysis.
Xenobiotica. 2018 May;48(5):506-532. doi: 10.1080/00498254.2017.1328148. Epub 2017 May 30. https://www.ncbi.nlm.nih.gov/pubmed/28481715
Citations 10
Reference articles
1.Analysis the prognostic values of solute carrier (SLC) family 39 genes in gastric cancer.
Am J Transl Res. 2019. --> Survival analysis, HR, P-val Figure 4!
2.The association between the expression of solute carrier transporters and the prognosis of pancreatic cancer.
Cancer Chemotherapy and Pharmacology. September 2013. --> Table 2-4!
Etc
Web-based tools/databases - A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data
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