第五章 討論與結論
5.2 結論
Microarray 技術的發展，提供生物醫學專家快速的累積基因表現的研究資料。這些數據 有高度的再利用性，可供其他研究人員進行多樣化的分析。相對的，資訊的爆炸產生了 另一些方面的需求，研究人員在經過實驗後可能得到一長串的可疑基因 list，正確的幫 基因做詳細的註解，成為一件重要的事情。以前生物醫學專家在經過複雜的實驗後會得 到少量的幾個可疑基因，以人工查詢這幾個基因是非常簡單的事情，但由於Microarray 的出現，使得可疑基因的數量暴增，幫基因做註解的工作變的相對複製。此外，不同技 術的Microarray 資料，要如何對照研究也是一個難題。DIPLEX 的開發完成，幫助我們 自動化產生基因註解資料，並提供與Pathway 資訊的整合以及不同平台 Microarray 基因 的比對工具，進而實行多樣的分析比較，並提供相關的基因表現數據做參考。然而，
DIPLEX 還有許多進步的空間，目前的資料只有以人類為主，未來的目標將著重在擴充 更多的物種，囊括更多的基因表現數據與Pathway 的資訊，以及改善系統效能。使用者 介面也是另一項發展的重心，一個好的網站必須不斷的改進使用者介面，讓使用者能更 快掌握到所需要的資訊，以及讓人一眼就明白的資料呈現方式。希望DIPLEX 能發展成 為生物資訊的重要網站。
參考文獻
中文參考文獻
中華民國行政院衛生署 http://www.doh.gov.tw
英文參考文獻
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電子資料
Affymetrix http://www.affymetrix.com ArrayExpress http://www.ebi.ac.uk/arrayexpress DDBJ http://www.ddbj.nig.ac.jp/
EMBL http://www.ebi.ac.uk/embl/
GenBank http://www.ncbi.nlm.nih.gov/GeneBank/
LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/
NCBI http://www.ncbi.nlm.nih.gov/
NCI panel of 60 human tumor cell lines http://dtp.nci.nih.gov/
OMIM http://www.ncbi.nlm.nih.gov/Omim/
RefSeq Statistics http://www.ncbi.nlm.nih.gov/LocusLink/
RSstatistics.html
Stanford SOURCE http://source.stanford.edu/
UniGene http://www.ncbi.nlm.nih.gov/UniGene/
UniProt http://www.pir.uniprot.org/
聯合國糧食及農業組織 http://www.fao.org/
附錄
CREATE TABLE `Acc2UG` (
`Acc` varchar(20) collate utf8_unicode_ci NOT NULL default '', `UniGene` varchar(20) collate utf8_unicode_ci NOT NULL default '', KEY `Acc` (`Acc`,`UniGene`),
KEY `UniGene` (`UniGene`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `ArrayExperiment`
--
CREATE TABLE `ArrayExperiment` ( `id` int(11) NOT NULL auto_increment,
`name` varchar(255) collate utf8_unicode_ci NOT NULL default '', `type` varchar(255) collate utf8_unicode_ci NOT NULL default '', `abstract` text collate utf8_unicode_ci NOT NULL,
PRIMARY KEY (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci AUTO_INCREMENT=4 ;
-- --- --
-- 資料表格式： `Clone2Acc` //Clone Image ID to GenBank Accession No.
--
CREATE TABLE `Clone2Acc` (
`CloneId` varchar(30) NOT NULL default '', `Collection` varchar(10) NOT NULL default '', `PlateNo` varchar(10) NOT NULL default '', `Row` varchar(10) NOT NULL default '', `Column` varchar(10) NOT NULL default '', `LibraryId` varchar(10) NOT NULL default '', `Species` varchar(10) NOT NULL default '', `Acc` varchar(255) NOT NULL default '', KEY `CloneId` (`CloneId`),
KEY `Acc` (`Acc`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COMMENT='Clone ID 2 GeneBankACC';
-- --- --
-- 資料表格式： `Gene2Kegg` //Gene ID to KEGG Pathway maps --
CREATE TABLE `Gene2Kegg` (
`LocusLink` int(10) NOT NULL default '0',
`KeggMap` varchar(255) collate utf8_unicode_ci NOT NULL default '', KEY `LocusLink` (`LocusLink`),
KEY `KeggMap` (`KeggMap`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `GoTerm` //Gene Ontology Terms --
CREATE TABLE `GoTerm` (
`id` int(11) NOT NULL default '0',
`name` varchar(255) collate utf8_unicode_ci NOT NULL default '', `term_type` varchar(55) collate utf8_unicode_ci NOT NULL default '', `go_id` varchar(255) collate utf8_unicode_ci NOT NULL default '', KEY `GoNum` (`go_id`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `HGNC` //HGNC table --
CREATE TABLE `HGNC` (
`HGNC_ID` varchar(10) collate utf8_unicode_ci NOT NULL default '', `Symbol` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Name` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Status` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Locus_Type` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Previous_Symbols` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Previous_Names` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Aliases` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`Chromosome` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Date_Approved` varchar(5) collate utf8_unicode_ci NOT NULL default '', `Date_Modified` varchar(5) collate utf8_unicode_ci NOT NULL default '', `Date_Name_Changed` varchar(5) collate utf8_unicode_ci NOT NULL default '', `Accession_Numbers` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Enzyme_ID` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`LocusLink_ID` varchar(255) collate utf8_unicode_ci NOT NULL default '', `MGD_ID` varchar(10) collate utf8_unicode_ci NOT NULL default '', `Misc_IDs` varchar(10) collate utf8_unicode_ci NOT NULL default '', `Pubmed_IDs` varchar(10) collate utf8_unicode_ci NOT NULL default '', `RefSeq_IDs` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`Gene_Family_Name` varchar(255) collate utf8_unicode_ci NOT NULL default '', `GDB` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`LocusLink` varchar(255) collate utf8_unicode_ci NOT NULL default '', `OMIM` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`RefSeq` varchar(255) collate utf8_unicode_ci NOT NULL default '', `SwissProt` varchar(255) collate utf8_unicode_ci NOT NULL default '', KEY `Approved_Symbol` (`Symbol`),
KEY `Approved_Name` (`Name`), KEY `Aliases` (`Aliases`),
KEY `Chromosome` (`Chromosome`), KEY `Enzyme_ID` (`Enzyme_ID`), KEY `LocusLink_ID` (`LocusLink_ID`), KEY `LocusLink` (`LocusLink`),
KEY `OMIM` (`OMIM`), KEY `RefSeq` (`RefSeq`), KEY `SwissProt` (`SwissProt`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `KeggTerm` //KEGG pathway map terms --
CREATE TABLE `KeggTerm` (
`keggid` varchar(20) collate utf8_unicode_ci NOT NULL default '', `keggterm` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`subclass` varchar(255) collate utf8_unicode_ci NOT NULL default 'Neurodegenerative Disorders',
`class` varchar(255) collate utf8_unicode_ci NOT NULL default 'Human Diseases', KEY `keggid` (`keggid`,`class`),
KEY `class` (`class`), KEY `subclass` (`subclass`), KEY `keggterm` (`keggterm`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `Loc2UG` //LocusLink (Entrez Gene ID) to UniGene ID
--
CREATE TABLE `Loc2UG` (
`LocusLink` varchar(20) character set utf8 collate utf8_unicode_ci NOT NULL default '', `UniGene` varchar(20) character set utf8 collate utf8_unicode_ci NOT NULL default '', KEY `LocusLink` (`LocusLink`),
KEY `UniGene` (`UniGene`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COMMENT='LocusLink to UniGene';
-- --- --
-- 資料表格式： `Loc2acc` // LocusLink (Entrez Gene ID) to GenBank Accession --
CREATE TABLE `Loc2acc` (
`LocusLink` int(10) NOT NULL default '0',
`Acc` varchar(20) collate utf8_unicode_ci NOT NULL default '', `gi_num` varchar(20) collate utf8_unicode_ci NOT NULL default '0', `sequence_type` varchar(10) collate utf8_unicode_ci NOT NULL default '', `protein_accession` varchar(20) collate utf8_unicode_ci NOT NULL default '', `tax_id` int(10) NOT NULL default '0',
KEY `LocusLink` (`LocusLink`), KEY `Acc` (`Acc`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `Loc2ref` //LocusLink (Entrez Gene ID) to RefSeq ID --
CREATE TABLE `Loc2ref` (
`LocusLink` int(10) NOT NULL default '0',
`Refseq` varchar(20) collate utf8_unicode_ci NOT NULL default '', `gi_num` varchar(20) collate utf8_unicode_ci NOT NULL default '0', `review_status` varchar(20) collate utf8_unicode_ci NOT NULL default '',
`protein_accession` varchar(20) collate utf8_unicode_ci NOT NULL default '', `tax_id` int(10) NOT NULL default '0',
KEY `LocusLink` (`LocusLink`), KEY `Refseq` (`Refseq`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `SAGELongTag2UG`
--
CREATE TABLE `SAGELongTag2UG` (
`UniGene` varchar(20) character set utf8 collate utf8_unicode_ci NOT NULL default '', `SAGELongTag` varchar(20) character set utf8 collate utf8_unicode_ci NOT NULL default '',
PRIMARY KEY (`SAGELongTag`), KEY `UniGene` (`UniGene`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 PACK_KEYS=0;
-- --- --
-- 資料表格式： `SAGEShortTag2UG`
--
CREATE TABLE `SAGEShortTag2UG` (
`UniGene` varchar(20) character set utf8 collate utf8_unicode_ci NOT NULL default '', `SAGEShortTag` varchar(20) character set utf8 collate utf8_unicode_ci NOT NULL default '',
PRIMARY KEY (`SAGEShortTag`), KEY `UniGene` (`UniGene`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-- --- --
-- 資料表格式： `biocarta_name` //Biocarta Pathway maps --
CREATE TABLE `biocarta_name` (
`PathwayID` varchar(255) collate utf8_unicode_ci NOT NULL default '', `PathwayName` text collate utf8_unicode_ci NOT NULL,
`WebAddress` text collate utf8_unicode_ci NOT NULL, PRIMARY KEY (`PathwayID`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `gene2biocarta` //Gene ID to BioCarta pathway maps --
CREATE TABLE `gene2biocarta` (
`PathwayID` varchar(255) collate utf8_unicode_ci NOT NULL default '', `GeneID` varchar(255) collate utf8_unicode_ci NOT NULL default '', KEY `GeneID` (`GeneID`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `gene2go` //Gene ID to Gene Ontology --
CREATE TABLE `gene2go` (
`tax_id` varchar(10) collate utf8_unicode_ci NOT NULL default '', `gene_id` int(10) NOT NULL default '0',
`go_id` varchar(255) collate utf8_unicode_ci NOT NULL default '', `evidence` varchar(10) collate utf8_unicode_ci NOT NULL default '', `go_qualifier` varchar(20) collate utf8_unicode_ci NOT NULL default '', `go_description` text collate utf8_unicode_ci NOT NULL,
KEY `gene_id` (`gene_id`), KEY `go_id` (`go_id`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `gene_info`
--
CREATE TABLE `gene_info` (
`tax_id` varchar(255) collate utf8_unicode_ci NOT NULL default '', `GeneID` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Symbol` varchar(255) collate utf8_unicode_ci NOT NULL default '', `LocusTag` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Synonyms` varchar(255) collate utf8_unicode_ci NOT NULL default '', `dbXrefs` varchar(255) collate utf8_unicode_ci NOT NULL default '', `chromosome` varchar(255) collate utf8_unicode_ci NOT NULL default '', `map_location` varchar(255) collate utf8_unicode_ci NOT NULL default '', `description` varchar(255) collate utf8_unicode_ci NOT NULL default '', `type_of_gene` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Symbol_authority` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Name_authority` varchar(255) collate utf8_unicode_ci NOT NULL default '', `Nomenclature_status` varchar(255) collate utf8_unicode_ci NOT NULL default '', KEY `tax_id` (`tax_id`),
KEY `GeneID` (`GeneID`), KEY `Symbol` (`Symbol`), KEY `Synonyms` (`Synonyms`), KEY `dbXrefs` (`dbXrefs`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;
-- --- --
-- 資料表格式： `mim2gene`
--
CREATE TABLE `mim2gene` (
`OMIM` varchar(255) collate utf8_unicode_ci NOT NULL default '',
`GeneID` varchar(255) collate utf8_unicode_ci NOT NULL default '', `type` varchar(255) collate utf8_unicode_ci NOT NULL default '', KEY `GeneID` (`GeneID`),
KEY `OMIM` (`OMIM`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;