Using the random walk with restart (RWR) algorithm, distances between input genes and pathway genes are calculated. if the HUGO Gene Nomenclature Committee (HGNC) symbols for interacting genes were not provided, conversion of provided gene identifiers to HGNC symbols using biomaRt (Durinck et al., 2009) was performed; (2.) Immune signaling by RIG-I-like receptors. 8 (11), 597607. Endocrinol. The hippo pathway effector YAP regulates motility, invasion, and castration-resistant growth of prostate cancer cells. The processed data are then used for active subnetwork search. ORA methods are also independent of the values associated with these genes, such as fold changes or p values. How to get KEGG pathway names from a list of 'ko' IDs? 2013, 436307436307. Nucleic Acids Res. 96 (4), 12611296. 14 (9), 9941008. Search box for searching map objects by IDs or aliase, KEGG identifier search with OR operation for multiple IDs, Plus sign allows input of user data in the form of KEGG Mapper Color tool, Module list in selected metabolic pathways, Reaction module list in overview (01200s) metabolic pathways, Network list in selected reference and human pathways linking to network variation maps, Links to related Brite hierarchies and Brite tables. : GTEx compendium Human tissue compendium (Novartis) Global Cancer Map (Broad Institute) NCI-60 cell lines (National Cancer Institute): Advanced query: Further investigate these 42 genes : Gene families ? In addition, the reference global maps are drawn with coloring to distinguish eleven functional categories 09101 to 09111 in. I need the get the list of gene names involved in glycolysis (to put an example). The researcher can get an overview of the alterations of genes in a pathway via the KEGG pathway graph. 6. (C) Heat map of pathway scores per subject. Wang S, Liang X, Guo R, Gong J, Zhong X, Liu Y, Wang D, Hao Y, Hu B. Ann Transl Med. The researcher is therefore able to choose between the different algorithms to obtain the optimal results. (2009). Curr. 4 (6), 174. doi: 10.4172/2155-9899.1000174, Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdottir, H., Tamayo, P., Mesirov, J. P. (2011). doi: 10.1016/j.trsl.2015.07.003, Saxena, M., Yeretssian, G. (2014). U. S. A. doi: 10.1038/nrurol.2014.196, Fortney, K., Kotlyar, M., Jurisica, I. The thickness of the edges between nodes corresponds to the kappa statistic between the two terms. Most commonly used pathway analysis methods are overrepresentation analysis (ORA) and functional class scoring (FCS). that the GSEA method can read. Brief descriptions of all pathways relevant to CRC are provided in Table 2. Lancet Oncol. Nucleic Acids Res. 62 (10), 28762885. All of these many protocols enable the user to take advantage of the full breadth of the functionality provided by KEGG. You can access KEGG API via Perl, Ruby, Python or Java. We would like to note that these results partly explain why taking interaction information into account results in enhanced enrichment results. Description This function gets a list of organisms in the KEGG database. doi: 10.1007/s00262-004-0653-2, Lee, S. H., Chang, D. K., Goel, A., Boland, C. R., Bugbee, W., Boyle, D. L., et al. doi: 10.3892/ol.2018.7735, Zhao, S., Zhang, Y., Zhang, Q., Wang, F., Zhang, D. (2014). KEGG GENES can be retrieved by giving identifiers of outside databases: NCBI-ProteinID (INSDC accession), NCBI-GeneID (Entrez Gene ID) and UniProt accession Gene expression network analysis and applications to immunology. The third dataset (GSE55945) compared the expression profiles of prostate tissue from 13 prostate cancer patients versus 8 controls using the Affymetrix Human Genome U133 Plus 2.0 Array platform. For a given list of significantly altered genes, an active subnetwork is defined as a group of interconnected genes in a protein-protein interaction network (PIN) that predominantly consists of significantly altered genes. The nuclear factor-kappaB pathway controls the progression of prostate cancer to androgen-independent growth. High-throughput technologies revolutionized biomedical research by enabling comprehensive characterization of biological systems. Gene Despite the fact that Biogrid has more than double the interactions of IntAct and 3 times the interactions of GeneMania, it remarkably does not contain half of the interactions they contain, implying this lack of overlap between PINs may affect pathfindR results. WebThe Pathways and Gene Interactions graph accompanies the "Gene Interactions" track and displays a detailed gene interaction and pathway graph based on data collected from two sources: curated pathway/protein-interaction databases and interactions found through text mining of PubMed abstracts. Hereby, we present pathfindR, another approach exploiting protein-protein interaction information and the first R package for active-subnetwork-oriented pathway enrichment analyses for class comparison omics experiments. EnrichNet: network-based gene set enrichment analysis. The role of cyclic nucleotide signaling pathways in cancer: targets for prevention and treatment. Supplementary Datasheet 2 | The unfiltered results of enrichment analyses using all the different methods on each of the datasets. (2017). doi: 10.1002/jcb.10683, Wen, Y. B., Dahut, W. L. (2009). Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Moreover, it is known that pathways in pathway databases may be strongly biased by some classes of genes or phenotypes that are popular targets, such as cancer signaling (Liu et al., 2017a). (2010). Finally, the significance of each pathway-level statistic is assessed, and significant pathways are determined. World J. Gastrointest. The tidyverse is convenient for working with data.frames. Cellular Processes Nucleic Acids Res. How i can get a list of KEGG pathways and its list of genes? To learn more, see our tips on writing great answers. Bioinformatics applications for pathway analysis of microarray data. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. 22 (2), 490500. doi: 10.1186/ar2729, Moradi-Marjaneh, R., Hassanian, S. M., Fiuji, H., Soleimanpour, S., Ferns, G. A., Avan, A., et al. The GMT (Gene Matrix Transposed) file format All High-quality GO gene sets were obtained from GO2MSIG (Powell, 2014) web interface (http://www.go2msig.org/cgi-bin/prebuilt.cgi?taxid=9606) in GMT format. The median percentages of RA-associated genes of the enriched pathways of pathfindR was higher than the median percentages of SPIA (2.43% vs. 0.96% for the 0.05 cutoff, 2.5% vs. 0.61% for the 0.1 cutoff, and 2.27% vs. 0.67% for the 0.25 cutoff). (2015). Get PI3K-AKT-mTOR signaling in prostate cancer progression and androgen deprivation therapy resistance. The pathfindR R (https://www.R-project.org/) package was developed based on a previous approach developed by our group for genome-wide association studies (GWASes): Pathway and Network-Oriented GWAS Analysis (PANOGA) (Bakir-Gungor et al., 2014). In the GMT format, each row represents a gene set. With pathfindR, we aimed to extend the approach of PANOGA to omics analyses and provide novel functionality. Csardi, G., Nepusz, T. (2006). If the score decreases, the change is accepted with a probability proportional to the temperature parameter that decreases in each step. Chem. This dataset will be referred to as RA. 53 (2), 105119. 36 (9), e48. 22 (8), 13131327. A separate confirmation of disease-relatedness was provided by analysis of the distributions of the percentage of disease genes in the identified pathways. Bioinformatics 27 (12), 17391740. To assess the number of pathways identified to be enriched by pathfindR, we performed analyses using actual and permuted data of different sizes. doi: 10.1049/iet-syb.2008.0155, Quionez-Flores, C. M., Gonzlez-Chvez, S. A., Pacheco-Tena, C. (2016). 38:W652-W656. A network-based method for predicting disease-causing genes. On the right bottom, a table summarizing the results is provided. Bioinformatics (Oxford, England) 28 (18), i451i457. As stated before, for the RA dataset, only pathfindR and SPIA identified significant pathways. Finally, temperature is the current temperature. (2009). The enrichment tests use the genes in the PIN as the gene pool (i.e., background genes). pathway 26k views WebIn KEGG, pathways are represented in XML files that contain genes and gene groups, such as protein complexes as entries and interactions as entry pairs. Nucleic Acids Res. 11 (2), R13. Advances in glucose metabolism research in colorectal cancer. Genet. TNF- promotes colon cancer cell migration and invasion by upregulating TROP-2. All authors were involved in the writing of the manuscript and read and approved the version being submitted. It is a self-sufficient, integrated resource consisting of genomic, chemical, and network information, with cross-references to numerous outside databases. (2012). 13 (7), 815827. Bookshelf Using the in-house script, the XML files were parsed; the interactions were added as undirected pairs, while interaction types were disregarded. How can I download KEGG pathways for the Arabidopsis genome in a CSV file? PLoS Genet. The PI3K/Akt/PTEN/mTOR pathway: a fruitful target for inducing cell death in rheumatoid arthritis? WebThe gene sets can be downloaded as NCBI (Entrez) Gene Identifiers or HUGO (HGNC) Gene Symbols. J Oncol. all PINs were formatted as SIFs. It only takes a minute to sign up. 34 (Database issue), D535D539. BioCarta. The VEGF signaling pathway in cancer: the road ahead. Epilepsy Res. This explains the high number of pathways obtained using the KEGG PIN. Eds. Sci. KEGG Pathway Map (Help) This package extends the use of the active-subnetwork-oriented pathway analysis approach to omics data. 45 (18), 15481553. get The distributions of disease-related gene percentages in pathways identified by each tool in the three different datasets, filtered by the adjusted-p value thresholds of 0.05, 0.1, and 0.25, are presented in Figure 5. doi: 10.1371/journal.pone.0154415, Bigelow, K., Nguyen, T. A. Ann. 4 (1), 4457. Int. Pathway enrichment was considered significant if FDR was <0.05. Hence, this fuzzy approach allows a pathway to be a member of multiple clusters. Akil, H., Perraud, A., Jauberteau, M.-O., Mathonnet, M. (2016). Asian J. Androl. Color indicates the log10(lowest-p) value; the more it shifts to red, the more significantly the pathway is enriched. Value. Gene A spatiotemporal hypothesis for the regulation, role, and targeting of AMPK in prostate cancer. doi: 10.1093/nar/gkw1102, Chiffoleau, E. (2018). Biomed. Federal government websites often end in .gov or .mil. (2015). Curr Protoc Bioinformatics. doi: 10.1093/bioinformatics/bts265, Berridge, M. J. BMC Bioinformatics 5, 100. doi: 10.1186/1471-2105-5-100, Bristow, R. G., Ozcelik, H., Jalali, F., Chan, N., Vesprini, D. (2007). So later I can use R to work manually. NF-kappa B in rheumatoid arthritis: a pivotal regulator of inflammation, hyperplasia, and tissue destruction. The results obtained using the different tools and literature support for the identified pathways (where applicable) are presented in Table 3. Cancer 107 (4), 513519. Curr. The PI3 kinase signaling pathway in prostate cancer. Here I show you how to use the DAVID functional annotation resource to easily do gene ontology and KEGG pathway enrichment from a gene list. The first dataset (GSE15573) aimed to characterize and compare gene expression profiles in the peripheral blood mononuclear cells of 18 rheumatoid arthritis (RA) patients versus 15 healthy subjects using the Illumina human-6 v2.0 expression bead chip platform. The enrichment p values were adjusted using the FDR method. (A) Clustering graph, each color displaying the clusters obtained for PCa. Additionally, it provides numerous improvements and useful new features. MSigDB Collections doi: 10.1093/nar/gkj109, Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., et al. KEGG - Bioconductor MAP kinases and prostate cancer. Int. J. Immunol. Tropomyosin-related kinase B/brain derived-neurotrophic factor signaling pathway as a potential therapeutic target for colorectal cancer. Identification of possible pathogenic pathways in Behcets disease using genome-wide association study data from two different populations. They can let insignificant genes between two clusters of significant genes to create a single connected active subnetwork. doi: 10.3892/ol.2016.5431, Dittrich, M. T., Klau, G. W., Rosenwald, A., Dandekar, T., Muller, T. (2008). For a overview of all availabl pathway names in a specific organism use the getKEGGPathwayOverview function. Software Internet Rep. 2 (3), 117120. Medicine (Baltimore). Phosphatidic acid, phospholipase D and tumorigenesis. Urol. Oncotarget 8 (7), 1186811876. This unit describes protocols for using KEGG, focusing on molecular network information in KEGG PATHWAY, KEGG BRITE, and KEGG MODULE, perturbed molecular networks in KEGG DISEASE and KEGG DRUG, molecular building block information in KEGG GENES and KEGG LIGAND, and a mechanism for linking genomes to molecular networks in KEGG ORTHOLOGY (KO). J. 14 (11), 683696. For the greedy and simulated annealing active subnetwork search algorithms, the search and enrichment processes are executed several times. doi: 10.1073/pnas.0506580102, Sumitomo, S., Nagafuchi, Y., Tsuchida, Y., Tsuchiya, H., Ota, M., Ishigaki, K., et al. To analyze the performance of pathfindR, we used three gene expression datasets. doi: 10.3748/wjg.v22.i2.490, PubMed Abstract | CrossRef Full Text | Google Scholar, Amgalan, B., Lee, H. (2014). Surg. Hsing, A. W., Gao, Y. T., Chua, S., Jr., Deng, J., Stanczyk, F. Z. Transl. doi: 10.3389/fimmu.2014.00327, Segui, B., Andrieu-Abadie, N., Jaffrezou, J. P., Benoist, H., Levade, T. (2006). 8 (9), R183. Immunol. While they are widely used, there are drawbacks to conventional pathway analysis methods. Res. Here is the solution, How to do vice verse, if i want to find all pathways associated with a list of genes using R or python? Reference pathway (KO): blue boxes are hyperlinked to KO entries that are selected from the original version. Initially, the input is filtered so that all p values are less than or equal to the given threshold (default is 0.05). Supplementary Figure 1 | Venn diagram of enrichment results obtained through pathfindR analyses with all available PINs. How can I extract gene names for a metabolic pathway pathfindR also allows for clustering of related pathways. How can I do this not using online web (2015). Forty-eight (48%) of these enriched pathways were relevant to CRC biology, as supported by literature. 2005 Oct;Chapter 1:Unit 1.12. doi: 10.1002/0471250953.bi0112s11. How do I perform a pathway related grouping of genes? WebParsing a list of gene sets from a flat text file in GMT format. doi: 10.1038/nprot.2009.97, Edgar, R., Domrachev, M., Lash, A. E. (2002). 68 (16), 67626769. 14 (1), 9099. Nucleic Acids Res. Transcriptional hallmarks of cancer cell lines reveal an emerging role of branched chain amino acid catabolism. Lipid For the PCa dataset, 1,240 DEGs were identified (Supplementary Data Sheet 1). See? Insulin signaling in insulin resistance states and cancer: a modeling analysis. doi: 10.1016/j.bbcan.2014.09.008, Del Prete, A., Salvi, V., Sozzani, S. (2014). Therefore, researchers face a challenge posed by high-throughput experiments: extracting relevant information that allows them to understand the underlying mechanisms from a long list of genes. Rev. The code of the pathfindR package is deposited in a GitHub repository (https://github.com/egeulgen/pathfindR) along with a detailed wiki, documenting the features of pathfindR in detail. Upon clustering, 14 clusters were identified (Figures 3A, B). Want more? The role of choline in prostate cancer. Curr Protoc Bioinformatics. Role of Th17 cells in human autoimmune arthritis. (2016). doi: 10.1093/nar/gkx1132, Fajardo, A. M., Piazza, G. A., Tinsley, H. N. (2014). Homologous recombination and prostate cancer: a model for novel DNA repair targets and therapies. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies. doi: 10.1002/ijc.22862, Siddiqui, N., Borden, K. L. (2012). doi: 10.2174/1389200211314090006, Gonnissen, A., Isebaert, S., Haustermans, K. (2013). The above findings indicate that incorporating interaction information prior to enrichment analysis results in better identification of disease-related mechanisms. Bioinformatics 20 (10), 15171521. Neither GSEA nor GSEAPreranked yielded any significant pathways for the CRC dataset. Careers. The results demonstrate that literature-supported disease-related pathways ranked higher in our approach compared to the others. Cancer 8 (11), 835850. Moreover, through a scoring function, the overall activity of each pathway in each sample can be estimated. doi: 10.1136/ard.53.5.287, Powell, J. Therefore, the PIN obtained through KEGG pathway interactions are biased. Identifying differentially regulated subnetworks from phosphoproteomic data. Cell Mol. Methods 132, 1925. Tumor antigen-specific T helper cells in cancer immunity and immunotherapy. This function delievers a vector with KEGG pathway information. How can I download KEGG pathways for the Arabidopsis genome in a CSV file? HHS Vulnerability Disclosure, Help Arthritis Res. The KEGG pathway XML files were obtained using the official KEGG Application Programming Interface (API) which is a REST-style interface to the KEGG database resource. doi: 10.4155/fmc.15.55, Malemud, C. J. Rev. BMC Bioinformatics 11, 351. doi: 10.1186/1471-2105-11-351. doi: 10.1002/jcp.26273, Mosesson, Y., Mills, G. B., Yarden, Y. A., Jiang, Z. For the CRC dataset, 1,356 DEGs were identified (Supplementary Data Sheet 1). 4 (8), 11841191. A. Simulated annealing and genetic algorithms are heuristic methods that do not make any assumptions on the active subnetwork model. is a tab delimited file format that describes gene sets. Microbial infection and rheumatoid arthritis. doi: 10.1016/S1470-2045(05)70168-6, Fang, S., Fang, X. WebIs their a way to extract a list of genes present in a KEGG pathway. Copyright 2019 Ulgen, Ozisik and Sezerman. The relevancy of 31 out of 78 (39.74%) pathways was supported by literature, briefly stated in Table 1. Biol. Carbohydrate Mol. These gene-level statistics are then aggregated into a pathway-level statistic for each pathway. mTOR pathway in colorectal cancer: an update. doi: 10.1093/bioinformatics/btm294, Gwinner, F., Boulday, G., Vandiedonck, C., Arnould, M., Cardoso, C., Nikolayeva, I., et al. 53 (5), 287288. doi: 10.1111/j.1365-2796.2009.02099.x, Pickup, M. W., Mouw, J. K., Weaver, V. M. (2014). 6 (5), 322327. Size of a node corresponds to its log(lowest_p). To determine the gene set enrichment, each gene set is then tested for overrepresentation in the subnetwork. Each KEGG pathway has a name and identifier. For this dataset, DAVID identified 20 significant pathways, 15 of which were also found by pathfindR (4 out of the remaining 5 were not supported by literature to be relevant to CRC). Acta 1758 (12), 21042120. (2007). (2005). (B) Boxplots for all the results filtered for adjusted-p 0.1. You have to use the NOD-like receptors: master regulators of inflammation and cancer. This results in the identification of phenotype-associated connected significant subnetworks. Novel sphingolipid-based cancer therapeutics in the personalized medicine era. Curr. Bioinformatics 25 (1), 7582. Consortium. We propose that directly performing pathway analysis on a gene set is not completely informative because this approach reduces gene-phenotype association evidence by ignoring information on interactions of genes. The KEGG PATHWAY database is a collection of manually drawn graphical diagrams, called KEGG pathway maps, for metabolic pathways, signaling pathways, pathways involved in various cellular processes and organismal systems, and perturbed pathways associated with human diseases. Acta 1773 (5), 642652. (2017). 16 (3), 378386. A. With pathfindR, our aim was likewise to exploit interaction information to extract the most relevant pathways. The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. Knights, A. J., Funnell, A. P. W., Crossley, M., Pearson, R. C. M. (2012). Adverb for when a person has never questioned something they believe. Front. Thank you. These percentages show great variability but support the literature search results in assessing the disease-relatedness of the enriched pathways. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Adv. Biol. doi: 10.1016/S1471-4892(03)00037-7, Liu, L., Wei, J., Ruan, J. J. Each node is an enriched pathway. RAS signaling pathways, mutations and their role in colorectal cancer. # WAYS TO DEFINE GENE SETS ACCORDING TO HUMAN KEGG PATHWAYS, http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats, http://www.genome.jp/kegg/catalog/org_list.html. KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge of the molecular interaction, reaction and relation networks These common pathways included general cancer-related pathways, such as pathways in cancer, proteoglycans in cancer, MAPK signaling pathway, Ras signaling pathway, Hippo signaling pathway, mTOR signaling pathway, Toll-like receptor signaling pathway, Wnt signaling pathway, and adherens junction. Rev. The acceptability of worse solutions allows a global search and escaping from local optima. Physiol. Using the genes in the PIN instead of the whole genome is more appropriate and provides more statistical strength because active subnetworks are identified using only the genes in the PIN. RNASeqRData GO 1.9k views An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Protoc. In May 2023, Frontiers adopted a new reporting platform to be Counter 5 compliant, in line with industry standards. Rev. The x axis indicates subjects, whereas the y axis indicates representative pathways. PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data. As gene sets, KEGG pathways were used. This algorithm considers addition of a node within a specified distance d to the current subnetwork. WebYou can use KEGG API to get all genes in a KEGG pathway. Introduction Sometimes there is quite a long list of genes to interpret after a differential expression analysis, and it is usually infeasible to go through the list one gene at a time trying to understand its biological function. Unable to load your collection due to an error, Unable to load your delegates due to an error. Front. Ras signaling in prostate cancer progression. Figure 5 Distributions of disease-associated genes in the enriched pathways. Interleukin-17: a promoter in colorectal cancer progression. All datasets were obtained via the Gene Expression Omnibus (GEO) (Edgar et al., 2002). WebHuman Gene Set: KEGG_GLYCOLYSIS_GLUCONEOGENESIS. pathfindR: an R package for pathway enrichment analysis utilizing active subnetworks. The default search method in pathfindR is greedy algorithm with a search depth of 1 and maximum depth of 1. By summarizing results over the iterations and identifying consistently enriched pathways, the stochasticity of these algorithms is overcome. After preprocessing, which included log2 transformation and quantile normalization, differential expression testing via a moderated t test using limma (Ritchie et al., 2015) was performed. Bioinformatics 12 (4), 320328. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Position in cell cycle controls the sensitivity of colon cancer cells to nitric oxide-dependent programmed cell death. doi: 10.1093/bioinformatics/bts389, Goffin, V., Hoang, D. T., Bogorad, R. L., Nevalainen, M. T. (2011). Cancer 121 (7), 14241432. The x axis corresponds to fold enrichment values, while the y axis indicates the enriched pathways. These significantly enriched pathways per all filtered subnetworks are then aggregated by keeping only the lowest adjusted p value for each pathway if a pathway was found to be significantly enriched in the enrichment analysis of more than one subnetwork. 3. Global/overview Initially identifying active subnetworks in a list of significant genes and then performing pathway enrichment analysis of these active subnetworks efficiently exploits interaction information between the genes. Finally, the representative pathway for each cluster is assigned as the pathway with the lowest adjusted p value. All of the datasets were processed using R to obtain (1) a list containing the genes involved in each given gene set/pathway (hence, each element of the list is named by the gene set ID and is a vector of gene symbols located in the given gene set/pathway) and (2) a list containing the descriptions for each gene set/pathway (i.e., a list linking gene set IDs to description). Pathway The researcher is also able to choose from numerous built-in gene sets, listed above, and can also provide a custom gene set resource. VEGF inhibitors and prostate cancer therapy. You can use KEGG REST API for extracting gene names from the pathway. (2000). 64 (12), 42274234. J. Autoimmun. (2012). 5, 327327. These genes will be referred to as RA Genes. For the CRC and PCa datasets, the Cancer Gene Census (CGC) genes from the Catalogue of Somatic Mutations in Cancer (COSMIC, http://cancer.sanger.ac.uk, retrieved on 19.12.2018) were used. doi: 10.1038/ejhg.2014.158, Bakir-Gungor, B., Sezerman, O. U. Figure 1 Flow diagrams of the pathfindR methods. (2014). In the same scoring scheme, a Monte Carlo approach is used for the calibration of the scores of subnetworks against a background distribution. Genes 8 (10), 246. doi: 10.3390/genes8100246, Liu, M., Liberzon, A., Kong, S. W., Lai, W. R., Park, P. J., Kohane, I. S., et al. 167 (1), 6779. Additionally, pre-ranked GSEA was performed (GSEAPreranked) using the default settings. Protoc. doi: 10.1186/gb-2007-8-9-r183, Ideker, T., Ozier, O., Schwikowski, B., Siegel, A. F. (2002).

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