title: SubpathwayMiner: a software package for flexible identification of pathways.
abstract: With the development of high-throughput experimental techniques such as microarray, mass spectrometry and large-scale mutagenesis, there is an increasing need to automatically annotate gene sets and identify the involved pathways. Although many pathway analysis tools are developed, new tools are still needed to meet the requirements for flexible or advanced analysis purpose. Here, we developed an R-based software package (SubpathwayMiner) for flexible pathway identification. SubpathwayMiner facilitates sub-pathway identification of metabolic pathways by using pathway structure information. Additionally, SubpathwayMiner also provides more flexibility in annotating gene sets and identifying the involved pathways (entire pathways and sub-pathways): (i) SubpathwayMiner is able to provide the most up-to-date pathway analysis results for users; (ii) SubpathwayMiner supports multiple species ( approximately 100 eukaryotes, 714 bacteria and 52 Archaea) and different gene identifiers (Entrez Gene IDs, NCBI-gi IDs, UniProt IDs, PDB IDs, etc.) in the KEGG GENE database; (iii) the system is quite efficient in cooperating with other R-based tools in biology. SubpathwayMiner is freely available at http://cran.r-project.org/web/packages/SubpathwayMiner/.
authors.affiliation: College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, People's Republic of China.
authors.forename: Chunquan
authors.initials: C
authors.lastname: Li
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.forename: Yingbo
authors.initials: Y
authors.lastname: Miao
authors.forename: Qianghu
authors.initials: Q
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
authors.forename: Chun
authors.initials: C
authors.lastname: Xu
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Junwei
authors.initials: J
authors.lastname: Han
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Binsheng
authors.initials: B
authors.lastname: Gong
authors.forename: Liangde
authors.initials: L
authors.lastname: Xu
mesh_terms: D003196:Computer Graphics; D053858:Metabolic Networks and Pathways; D012984:Software
references.citation: Clin Cancer Res. 2006 Jan 15;12(2):369-75
references.pmid: 16428474
references.citation: Bioinformatics. 2008 Jun 15;24(12):1461-2
references.pmid: 18441000
references.citation: Nucleic Acids Res. 2004 May 17;32(9):2685-94
references.pmid: 15148356
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7
references.pmid: 16381885
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W621-6
references.pmid: 15980549
references.citation: BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S8
references.pmid: 17903289
references.citation: Clin Cancer Res. 2005 Oct 15;11(20):7264-72
references.pmid: 16243796
references.citation: Bioinformatics. 2004 Aug 4;20 Suppl 1:i200-7
references.pmid: 15262800
references.citation: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
references.pmid: 11309499
references.citation: PLoS One. 2008 Feb 20;3(2):e1651
references.pmid: 18297132
references.citation: Pathol Res Pract. 2008;204(5):295-304
references.pmid: 18358633
references.citation: BMC Cancer. 2005 Jul 06;5:73
references.pmid: 16000172
references.citation: Nucleic Acids Res. 2000 Oct 15;28(20):4021-8
references.pmid: 11024183
references.citation: BMC Bioinformatics. 2003 Nov 07;4:56
references.pmid: 14604444
references.citation: Clin Cancer Res. 2003 Feb;9(2):853-60
references.pmid: 12576459
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5
references.pmid: 17526522
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W633-7
references.pmid: 15980551
references.citation: Bioinformatics. 2006 Apr 15;22(8):967-73
references.pmid: 16492685
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W176-81
references.pmid: 17586825
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W741-8
references.pmid: 15980575
references.citation: Biochem Biophys Res Commun. 2005 Jul 22;333(1):35-41
references.pmid: 15936720
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W720-4
references.pmid: 16845106
references.citation: Nat Genet. 2008 Jun;40(6):707-9
references.pmid: 18500343
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Cancer Res. 2007 Nov 1;67(21):10389-96
references.pmid: 17974982
references.citation: Carcinogenesis. 2006 May;27(5):1018-23
references.pmid: 16332725
references.citation: Breast Cancer Res Treat. 2007 Dec;106(2):281-8
references.pmid: 17268812
references.citation: Rev Endocr Metab Disord. 2001 Aug;2(3):297-311
references.pmid: 11708294
references.citation: Pharmacol Rev. 2004 Sep;56(3):331-49
references.pmid: 15317907
references.citation: Genome Biol. 2008;9(12):R179
references.pmid: 19094223
references.citation: Mol Biol (Mosk). 2006 Nov-Dec;40(6):1047-54
references.pmid: 17209433
references.citation: Bioinformatics. 2005 Oct 1;21(19):3787-93
references.pmid: 15817693
references.citation: J Nucl Med. 2005 Sep;46(9):1414-20
references.pmid: 16157522
references.citation: Cancer Lett. 2008 Mar 18;261(2):147-57
references.pmid: 18171602
references.citation: Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):31-6
references.pmid: 11134512
references.citation: Brain Behav Immun. 2008 Mar;22(3):318-23
references.pmid: 17981009
references.citation: Int J Cancer. 2006 Dec 15;119(12):2827-31
references.pmid: 17036331
references.citation: Carcinogenesis. 2005 Nov;26(11):1988-98
references.pmid: 15975962
references.citation: Cancer Res. 2006 Nov 1;66(21):10357-64
references.pmid: 17079456
references.citation: BMC Bioinformatics. 2008 Jul 09;9:303
references.pmid: 18613966