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Dechao Bu, Haitao Luo, Peipei Huo, Zhihao Wang, Shan Zhang, Zihao He, Yang Wu, Lianhe Zhao, Jingjia Liu, Jincheng Guo and 5 more
Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class scoring), and PT (pathway topology) approaches are three generations of GSE methods along the timeline of development. Previous versions of KOBAS provided services based on just the ORA method. Here we presented version 3.0 of KOBAS, which is named KOBAS-i (short for KOBAS intelligent version). It introduced a novel machine learning-based method we published earlier, CGPS, which incorporates seven FCS tools and two PT tools into a single ensemble score and intelligently prioritizes the relevant biological pathways. In addition, KOBAS has expanded the downstream exploratory visualization for selecting and understanding the enriched results. The tool constructs a novel view of cirFunMap, which presents different enriched terms and their correlations in a landscape. Finally, based on the previous version's framework, KOBAS increased the number of supported species from 1327 to 5944. For an easier local run, it also provides a prebuilt Docker image that requires no installation, as a supplementary to the source code version. KOBAS can be freely accessed at http://kobas.cbi.pku.edu.cn, and a mirror site is available at http://bioinfo.org/kobas.
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Bu, D., Luo, H., Huo, P., Wang, Z., Zhang, S., He, Z., Wu, Y., Zhao, L., Liu, J., Guo, J., Fang, S., Cao, W., Yi, L., Zhao, Y. C., & Kong, L. (2021). KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Research, 49(W1), W317–W325. https://doi.org/10.1093/nar/gkab447
Bu, Dechao, et al. "KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis." Nucleic Acids Research, vol. 49, no. W1, 2021, pp. W317–W325, https://doi.org/10.1093/nar/gkab447.
Bu, Dechao, Haitao Luo, Peipei Huo, Zhihao Wang, Shan Zhang, Zihao He, Yang Wu, et al. "KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis." Nucleic Acids Research 49, no. W1 (2021): W317–W325. https://doi.org/10.1093/nar/gkab447.
Bu D., Luo H., Huo P. [и др.] KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis // Nucleic Acids Research. — 2021. — Vol. 49, № W1. — P. W317–W325. — URL: https://doi.org/10.1093/nar/gkab447
@article{bu2021kobasi,
title = {{KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis}},
author = {Dechao Bu and Haitao Luo and Peipei Huo and Zhihao Wang and Shan Zhang and Zihao He and Yang Wu and Lianhe Zhao and Jingjia Liu and Jincheng Guo and Shuangsang Fang and Wanchen Cao and Lan Yi and Yi Chen Zhao and Lei Kong},
journal = {Nucleic Acids Research},
year = {2021},
volume = {49},
number = {W1},
pages = {W317--W325},
doi = {10.1093/nar/gkab447},
url = {https://doi.org/10.1093/nar/gkab447}
}TY - JOUR AU - Bu, Dechao AU - Luo, Haitao AU - Huo, Peipei AU - Wang, Zhihao AU - Zhang, Shan AU - He, Zihao AU - Wu, Yang AU - Zhao, Lianhe AU - Liu, Jingjia AU - Guo, Jincheng AU - Fang, Shuangsang AU - Cao, Wanchen AU - Yi, Lan AU - Zhao, Yi Chen AU - Kong, Lei TI - KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis JO - Nucleic Acids Research VL - 49 IS - W1 SP - W317 EP - W325 PY - 2021 DA - 2021/05/09 DO - 10.1093/nar/gkab447 UR - https://doi.org/10.1093/nar/gkab447 ER -
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