Gene setあるいはSNP setを保存するには名前とコメントを入力し、保存をクリックして、選択したポイントで指定された遺伝子を含む新規のgene setを作成します.
アルゴリズム
データの抽出と前処理機能
Simbiotはデータの処理・解析にpeer-reviewedアルゴリズムを使用しています。エクスポート過程では下に示すBioconductor (Gentleman, Carey et al.
2004)ツールを利用しています：
- Affymetrix cDNA
chips: Bioconductor affy (Gautier, Cope et
al. 2004)
- Affymetrix SNP chips: Bioconductor crlmm (Carvalho,
Bengtsson et al. 2007)
- Illumina cDNA
microarrays: Bioconductor lumi (Du, Kibbe et al.
2008)
- Illumina SNP
microarrays: Bioconductor
beadarraySNP (Oosting, Lips et
al. 2007)
データ解析
データ解析では、peer-reviewedと標準の解析がデータ・独立形式が統合されています：
- クラスタリング：
Cluster 3.0 (de Hoon, Imoto et
al. 2004)、 Rを基本としたクラスタリング機能
- 標準統計：Rを基本としたクラスタリング機能
- 発現解析：
samr (Tusher, Tibshirani
et al. 2001)、Bioconductor
limma (Smyth 2004)とLPE (Jain, Thatte et
al. 2003)パッケージ
- タイムコース解析：
Bioconductor timecourse (Tai and Speed
2009)とmaSigPro
(Conesa, Nueda et
al. 2006)パッケージ
- SNP
Association study and linkage disequilibrium：
Bioconductor snpMatrix (Clayton and Leung
2007)パッケージ
- コピー数解析：
Bioconductor snapCGH (Marioni, Thorne et
al. 2006; Smith, Marioni et al. 2006)
リファレンス
Ashburner, M., C.
A. Ball, et al. (2000). "Gene ontology: tool for the unification of
biology. The Gene Ontology Consortium." Nat Genet 25(1): 25-9.
Boeckmann, B., A.
Bairoch, et al. (2003). "The SWISS-PROT protein knowledgebase and its
supplement TrEMBL in 2003." Nucleic Acids Res 31(1): 365-70.
Carvalho, B., H.
Bengtsson, et al. (2007). "Exploration, normalization, and genotype calls
of high-density oligonucleotide SNP array data." Biostatistics 8(2): 485-99.
Clayton, D. and H.
T. Leung (2007). "An R package for analysis of whole-genome association
studies." Hum Hered 64(1):
45-51.
Conesa, A., M. J.
Nueda, et al. (2006). "maSigPro: a method to identify significantly
differential expression profiles in time-course microarray experiments." Bioinformatics
22(9): 1096-102.
Consortium, U.
"The Universal Protein Resource (UniProt) in 2010." Nucleic Acids
Res 38(Database issue): D142-8.
de Hoon, M. J.,
S. Imoto, et al. (2004). "Open source clustering software." Bioinformatics
20(9): 1453-4.
Du, P., W. A.
Kibbe, et al. (2008). "lumi: a pipeline for processing Illumina
microarray." Bioinformatics 24(13):
1547-8.
Gautier, L., L.
Cope, et al. (2004). "affy--analysis of Affymetrix GeneChip data at the
probe level." Bioinformatics 20(3):
307-15.
Gentleman, R. C.,
V. J. Carey, et al. (2004). "Bioconductor: open software development for
computational biology and bioinformatics." Genome Biol 5(10): R80.
Hubbard, T. J.,
B. L. Aken, et al. (2009). "Ensembl 2009." Nucleic Acids Res 37(Database issue): D690-7.
Jain, N., J.
Thatte, et al. (2003). "Local-pooled-error test for identifying
differentially expressed genes with a small number of replicated
microarrays." Bioinformatics 19(15):
1945-51.
Kanehisa, M. and
S. Goto (2000). "KEGG: kyoto encyclopedia of genes and genomes." Nucleic
Acids Res 28(1): 27-30.
Marioni, J. C.,
N. P. Thorne, et al. (2006). "BioHMM: a heterogeneous hidden Markov model
for segmenting array CGH data." Bioinformatics 22(9): 1144-6.
Oosting, J., E.
H. Lips, et al. (2007). "High-resolution copy number analysis of
paraffin-embedded archival tissue using SNP BeadArrays." Genome Res
17(3): 368-76.
Sayers, E. W., T.
Barrett, et al. "Database resources of the National Center for
Biotechnology Information." Nucleic Acids Res38(Database issue): D5-16.
Smith, M. L., J.
C. Marioni, et al. (2006). "snapCGH: Segmentation, Normalization and
Processing of aCGH Data Users' Guide." Bioconductor.
Smyth, G. K.
(2004). "Linear models and empirical bayes methods for assessing
differential expression in microarray experiments." Stat Appl Genet Mol
Biol 3: Article3.
Tai, Y. C. and T.
P. Speed (2009). "On gene ranking using replicated microarray time course
data." Biometrics 65(1):
40-51.
Tusher, V. G., R.
Tibshirani, et al. (2001). "Significance analysis of microarrays applied
to the ionizing radiation response." Proc Natl Acad Sci U S A 98(9): 5116-21.
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