An In-depth Exploration: Unveiling the Computational Resources Utilized in Cancer Research
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Coker EA, Mitsopoulos C, Tym JE, Komianou A, Kannas C, Di Micco P et al. canSAR: update to the cancer translational research and drug discovery KnowledgeBase. Nucleic Acids Res. 2019; 47 (D1): D917–D922. doi: 10.1093/nar/gky1129, PMID 30496479.
Aguirre-Gamboa R, Trevino V. SurvMicro. SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis. Bioinformatics. 2014; 30 (11): 1630–1632. doi: 10.1093/bioinformatics/btu087, PMID 24519378.
Aguirre-Gamboa R, Gomez-Rueda H, Martínez-Ledesma E, Martínez-Torteya A, Chacolla-Huaringa R, Rodriguez-Barrientos A et al. SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis. PLOS ONE. 2013; 8 (9): e74250. doi: 10.1371/journal.pone.0074250, PMID 24066126.
Anaya J. OncoLnc: linking TCGA survival data to mRNAs, miRNAs, and lncRNAs. PeerJ Comput Sci. 2016; 2: e67. doi: 10.7717/peerj-cs.67.
Bader GD, Betel D, Hogue CW. BIND: the biomolecular interaction network database. Nucleic Acids Res. 2003; 31 (1): 248–250. doi: 10.1093/nar/gkg056, PMID 12519993.
Bahceci I, Dogrusoz U, La KC, Babur Ö, Gao J, Schultz N. PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. Bioinformatics. 2017; 33 (14): 2238–2240. doi: 10.1093/bioinformatics/btx149, PMID 28334343.
Complexica. (2016). Computational intelligence. Available at https://www.complexica.com/ narrow-ai-glossary/computational-intelligence [Accessed on December 2023]
Bhattacharya A, Cui Y, Somami R. SomamiR 2.0: a database of cancer somatic mutations altering microRNA–ceRNA interactions. Nucleic Acids Res. 2016; 44 (D1): D1005–D1010. doi: 10.1093/nar/gkv1220, PMID 26578591.
de Anda-Jáuregui G, Hernández-Lemus E. Computational oncology in the multi-omics era: state of the art. Front Oncol. 2020; 10: 423. doi: 10.3389/fonc.2020.00423, PMID 32318338.
Chin L, Andersen JN, Futreal PA. Cancer genomics: from discovery science to personalized medicine. Nat Med. 2011; 17 (3): 297–303. doi: 10.1038/nm.2323, PMID 21383744.
Blekherman G, Laubenbacher R, Cortes DF, Mendes P, Torti FM, Akman S et al. Bioinformatics tools for cancer metabolomics. Metabolomics. 2011; 7 (3): 329–343. doi: 10.1007/s11306-010-0270-3, PMID 21949492.
Borcherding N, Bormann NL, Voigt AP, Zhang W. TRGAted: A web tool for survival analysis using protein data in the Cancer Genome Atlas. F1000Res. 2018; 7: 1235. doi: 10.12688/f1000research.15789.2, PMID 30345029.
Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018; 68 (6): 394–424. doi: 10.3322/caac.21492, PMID 30207593.
Broeckling CD, Reddy IR, Duran AL, Zhao X, Sumner LW. MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Anal Chem. 2006; 78 (13): 4334–4341. doi: 10.1021/ac0521596, PMID 16808440.
Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK et al. UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia. 2017; 19 (8): 649–658. doi: 10.1016/j.neo.2017.05.002, PMID 28732212.
National Cancer Institute. (2023). Home: NCI Genomic Data Commons. [Online] Available at https://gdc.cancer.gov/
European Genome-phenome Archive. (2017). Home page. [Online] Available at https://ega-archive.org/.
COSMIC. (2023). COSMIC v99, released 28-NOV-23. [Online] Available at https://cancer. sanger.ac.uk/cosmic
cBioPortal for Cancer Genomics. (2021). Home page. [Online] Available at https://www.cbioportal.org/
Broad Institute. (2018). Cancer Program Scientific Tools and Resources. [Online] Available at https://www.broadinstitute.org/cancer/cancer-program-scientific-tools-and-resources
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C et al. canEvolve: a web portal for integrative oncogenomics. PLOS ONE. 2013 Feb 13; 8 (2): e56228. doi: 10.1371/journal.pone.0056228, PMID 23418540.
Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M et al. The UCSC cancer genomics browser: update 2015. Nucleic Acids Res. 2015; 43(Database issue): D812–D817. doi: 10.1093/nar/gku1073, PMID 25392408.
G6G Tech. (2021). G6G Directory of Omics and Intelligent Software. [Online] Available at https://www.g6g-softwaredirectory.com/bio/genomics/genetic-analysis/20773-CGWB.php
He X, Chang S, Zhang J, Zhao Q, Xiang H, Kusonmano K et al. MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res. 2008; 36 (Database issue; Suppl._1): D836–D841. doi: 10.1093/nar/gkm730, PMID 17890243.
SomamiR DB. (2023). Somatic mutations altering microRNA-ceRNA interactions. [Online] Available at https://compbio.uthsc.edu/SomamiR/
Liu C, Bai B, Skogerbø G, Cai L, Deng W, Zhang Y et al. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 2005; 33 (Database issue; Suppl. 1): D112–D115. doi: 10.1093/nar/gki041, PMID 15608158.
Packer BR, Yeager M, Staats B, Welch R, Crenshaw A, Kiley M et al. SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. Nucleic Acids Res. 2004; 32 (Database issue; Suppl. 1): D528–D532. doi: 10.1093/nar/gkh005, PMID 14681474.
Massachusetts General Hospital. (2022). Genomics of drug sensitivity in cancer. [Online] Available at https://www.cancerrxgene.org/
MD Anderson Cancer Center. (2021). canSAR.ai. [Online] Available at https://cansar.ai/
SourceForge. (2023). SASHIMI Files. [Online] Available at https://sourceforge.net/projects/ sashimi/files/SpecArray/ [Accessed on December 2023]
MSight SIB. (2023). Home page. [Online] Available at https://msight.sib.swiss/
George M. Church Laboratory. (2023). MapQuant-Suite Download Page. [Online] Available at https://arep.med.harvard.edu/MapQuant/download-forms/download-bin-msi.html
Thermo Fisher Scientific. (2014). Metabolomics data analysis. [Online] Available at https://www.thermofisher.com/in/en/home/industrial/mass-spectrometry/mass-spectrometry-learn ing-center/mass-spectrometry-applications-area/metabolomics-mass-spectrometry/metabolomics-data-analysis.html [Accessed on December 2023]
Scripps.edu. (2023). XCMS online usage instructions. [Online] Available at https://xcmsonline. scripps.edu/landing_page.php?pgcontent=documentation
Chong J, Yamamoto M, Xia J. MetaboAnalystR 2.0: from raw spectra to biological insights. Metabolites. 2019; 9 (3): 57. doi: 10.3390/metabo9030057, PMID 30909447.
Biomedical Informatics Institute. (2023). LOGpc. [Online] Available at https://bioinfo.henu. edu.cn/DatabaseList.jsp
GENT2. (2023). Introduction. [Online] Available at http://gent2.appex.kr/gent2/
Goswami CP, Nakshatri H. PROGgeneV2: enhancements on the existing database. BMC cancer. 2014 Dec; 14(1): 1–6.
Moffitt Cancer Center. (2023). Senior Adult Oncology Program Tools. [Online] Available at https://www.moffitt.org/for-healthcare-professionals/clinical-programs-and-services/senior-adult-oncology-program/senior-adult-oncology-program-tools/
Győrffy B. (2023). Kaplan-Meier plotter: what is the KM plotter? [Online] Available at http://kmplot.com/analysis/
Chen MJ, Li J, Wang Y, Akbani R, Lu Y, Mills GB, Liang H. TCPA v3.0: an integrative platform to explore the pan-cancer analysis of functional proteomic data. Mol Cell Proteomics. 2019; 18 (8): S15–S25.
TRGAted. (2014). Home. [Online] Available at https://nborcherding.shinyapps.io/TRGAted/
Madden SF, Clarke C, Stordal B, Carey MS, Broaddus R, Gallagher WM, et al. OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets. Mol Cancer. 2014; 13 (1): 1–1.
GEPIA 2. (2023). Single gene analysis. [Online] Available at http://gepia2.cancer-pku.cn/#index
MD Anderson Cancer Center. (2016). The Cancer Proteome Atlas. [Online] Available at https://bioinformatics.mdanderson.org/public-software/tcpa/
Chen X, Sun X, Hoshida Y. Survival analysis tools in genomics research. Hum Genomics. 2014; 8: 1–5.
UALCAN. (2022). Welcome to UALCAN [Online] Available at https://ualcan.path.uab.edu/
U.S. Environment Protection Agency. (2021). HAWC Resources. [Online] Available at https://www.epa.gov/risk/hawc-resources
DEMO Table Builder. (2023). Welcome to DEMO table builder! [Online] Available at https://table-builder.com/
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz Jr LA, Kinzler KW. Cancer genome landscapes. Science. 2013; 339 (6127): 1546–1558.
Cancer Regulome. (2017). Cancer Regulome Tools & Data. [Online] Available at https://explorer-cancerregulome.systemsbiology.net/
Yu KH, Fitzpatrick MR, Pappas L, Chan W, Kung J, Snyder M. Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction. Bioinformatics. 2018; 34 (2): 319–320.
Schlicker A, Michaut M, Rahman R, Wessels LF. OncoScape: exploring the cancer aberration landscape by genomic data fusion. Sci Rep. 2016; 6 (1): 28103.
National Cancer Institute. (2018). The Cancer Genome Atlas Program (TCGA). [Online] Available at https://www.cancer.gov/ccg/research/genome-sequencing/tcga
Cancer3D *v2. (2023). Cancer3d. [Online] Available at http://cancer3d.org/search
Koch A, De Meyer T, Jeschke J, Van Criekinge W. MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data. BMC Genomics. 2015; 16: 1–6.
Obermayer AN, Chang D, Nobles G, Teng M, Tan AC, Wang X, et al. PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. BMC Bioinformatics. 2023; 24 (1): 1–4.
National Cancer Institute. (2022). About the cancer imaging archive. [Online] Available at https://www.cancerimagingarchive.net/about-the-cancer-imaging-archive-tcia/
Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, et al. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003; 4 (4): 1–8.
Patel S, Lyons-Weiler J. caGEDA: a web application for the integrated analysis of global gene expression patterns in cancer. Appl Bioinformatics. 2004; 3 (1): 49–62.
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. CIBEX: center for information biology gene expression database. C R Biol. 2003; 326 (10–11): 1079–1082.
Shrestha S, Bhuvan KC, Blebil AQ, Teoh SL. Pharmacist involvement in cancer pain management: a systematic review and meta-analysis. J Pain. 2022; 23 (7): 1123–1142.
McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics. 2000; 16 (4): 404–405.
SWISS-MODEL. (2020). Home page. [Online] Available at https://swissmodel.expasy.org/
Liu T. (2013). Binding database home. [Online] Available at https://www.bindingdb.org/rwd/ bind/index.jsp
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, et al. The IntAct molecular interaction database in 2012. Nucleic Acids Res. 2012; 40 (D1): D841–D846.
Benton HP, Wong DM, Trauger SA, Siuzdak G. XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem. 2008; 80 (16): 6382–6389.
National Institutes of Health. (2023). Ingenuity Pathways Analysis (IPA). [Online] Available at https://www.nihlibrary.nih.gov/resources/tools/ingenuity-pathways-analysis-ipa
Aguirre-Gamboa R, Trevino V. SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis. Bioinformatics. 2014; 30 (11): 1630–1632. doi: 10.1093/bioinformatics/btu087, PMID 24519378.
Modhukur V, Iljasenko T, Metsalu T, Lokk K, Laisk-Podar T, Vilo J. MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data. Epigenomics. 2018; 10 (3): 277–288. doi: 10.2217/epi-2017-0118, PMID 29264942.
Hearne BJ, Teare MD, Butt M, Donaldson L. Comparison of Nottingham Prognostic Index and adjuvant online prognostic tools in young women with breast cancer: review of a single-institution experience. BMJ Open. 2015; 5 (1): e005576. doi: 10.1136/bmjopen-2014-005576, PMID 25628047.
Xie L, Wang L, Zhu W, Zhao J, Guo X. Editorial: bioinformatics tools (and web server) for cancer biomarker development. Front Oncol. 2020; 10: 599085. doi: 10.3389/fonc.2020.599085, PMID 33194766.
Netek R, Pour T, Slezakova R. Implementation of heat maps in geographical information system: exploratory study on traffic accident data. Open Geosci. 2018; 10 (1): 367–384. doi: 10.1515/geo-2018-0029.
MD Anderson Cancer Center. (2016). TCGA SpliceSeq. [Online] Available at https://bioinformatics.mdanderson.org/public-software/tcgaspliceseq/
TANRIC. (2022). The Atlas of non-coding RNA in Cancer. [Online] Available at https://bioinformatics.mdanderson.org/public-software/tanric/
Huang PJ, Lee CC, Tan BC, Yeh YM, Huang KY, Gan RC et al. Vanno: a visualization‐aided variant annotation tool. Hum Mutat. 2015; 36 (2): 167–174. doi: 10.1002/humu.22684, PMID 25196204.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215 (3): 403–410. doi: 10.1016/S0022-2836(05)80360-2, PMID 2231712.
DOI: https://doi.org/10.37628/ijippr.v9i2.949
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