SEAS: A System for SEED-Based Pathway Enrichment Analysis

被引：8
|
作者：
Mao, Xizeng [1 ]
Zhang, Yu [3 ,4 ]
Xu, Ying [1 ,2 ,3 ]
机构：
[1] Univ Georgia, Computat Syst Biol Lab, Dept Biochem & Mol Biol, Inst Bioinformat, Athens, GA 30602 USA
[2] Univ Georgia, BioEnergy Sci Ctr BESC, Athens, GA 30602 USA
[3] Jilin Univ, Coll Comp Sci & Technol, Changchun 130023, Peoples R China
[4] Jilin Univ, Key Lab Symbol Computat & Knowledge Engn, Minist Educ, Changchun 130023, Peoples R China
来源：
PLOS ONE | 2011年 / 6卷 / 07期
基金：
美国国家科学基金会;
关键词：
GENE-EXPRESSION DATA; GENOME ANNOTATION; RESOURCES; SERVER;
D O I：
10.1371/journal.pone.0022556
中图分类号：
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Pathway enrichment analysis represents a key technique for analyzing high-throughput omic data, and it can help to link individual genes or proteins found to be differentially expressed under specific conditions to well-understood biological pathways. We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specified organism against the pathways (or subsystems) in the SEED database, a popular pathway database for bacteria. SEAS maps a given set of genes of a bacterium to pathway genes covered by SEED through gene ID and/or orthology mapping, and then calculates the statistical significance of the enrichment of each relevant SEED pathway by the mapped genes. Our evaluation of SEAS indicates that the program provides highly reliable pathway mapping results and identifies more organism-specific pathways than similar existing programs. SEAS is publicly released under the GPL license agreement and freely available at http://csbl.bmb.uga.edu/similar to xizeng/research/seas/.
引用
收藏
页数：6
相关论文
共 50 条
  • [21] Need to Seed? Ecological, Genetic, and Evolutionary Keys to Seed-Based Wetland Restoration
    Kettenring, Karin M.
    Tarsa, Emily E.
    FRONTIERS IN ENVIRONMENTAL SCIENCE, 2020, 8
  • [22] Network-based Pathway Enrichment Analysis
    Liu, Lu
    Ruan, Jianhua
    2013 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM), 2013,
  • [23] Parallel Seed-Based Approach to Protein Structure Similarity Detection
    Chapuis, Guillaume
    Le Boudic-Jamin, Mathilde
    Andonov, Rumen
    Djidjev, Hristo
    Lavenier, Dominique
    PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2013), PT II, 2014, 8385 : 278 - 287
  • [24] A Seed-Based Diffusion Route to Monodisperse Intermetallic CuAu Nanocrystals
    Chen, Wei
    Yu, Rong
    Li, Lingling
    Wang, Annan
    Peng, Qing
    Li, Yadong
    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2010, 49 (16) : 2917 - 2921
  • [25] Seed-based authentication for mobile clients across multiple devices
    Chen, Longbin
    Chen, Li-Chiou
    Nassar, Nader
    INFORMATION SECURITY JOURNAL, 2018, 27 (01): : 29 - 41
  • [26] Calibrating Seed-Based Heuristics to Map Short Reads With Sesame
    Filion, Guillaume J.
    Cortini, Ruggero
    Zorita, Eduard
    FRONTIERS IN GENETICS, 2020, 11
  • [27] Automated Mapping of Sensorimotor Network for Resting State fMRI Data with Seed-Based Correlation Analysis
    de Oliveira, Bruno Goulart
    Filho, Jose Osmar Alves
    Esper, Nathalia Bianchini
    Guimaraes de Azevedo, Dario Francisco
    Franco, Alexandre R.
    XXVI BRAZILIAN CONGRESS ON BIOMEDICAL ENGINEERING, CBEB 2018, VOL. 2, 2019, 70 (02): : 537 - 544
  • [28] Comparative study on similarity metrics for seed-based analysis of functional connectivity photoacoustic tomography images
    Khodaei, Afsoon
    Nasiriavanaki, Mohammadreza
    PHOTONS PLUS ULTRASOUND: IMAGING AND SENSING 2017, 2017, 10064
  • [29] Bottlenecks to seed-based seagrass restoration reveal opportunities for improvement
    Unsworth, R. K. F.
    Bertelli, C. M.
    Coals, L.
    Cullen-Unsworth, L. C.
    den Haan, S.
    Jones, B. L. H.
    Rees, S. R.
    Thomsen, E.
    Wookey, A.
    Walter, B.
    GLOBAL ECOLOGY AND CONSERVATION, 2023, 48
  • [30] Preparation, packaging and storage of amaranthus seed-based traditional sweetmeats
    J Food Sci Technol, 2 (160-163):
12345