際際滷

際際滷Share a Scribd company logo

2013_08_30_Bioinformatics1_yes

Download as PPTX, PDF
Eunsil Yoon
Eunsil Yoon

蠍磯蓋 BioInformatics 螳 豌螳

1 of 17
Downloaded 22 times
BioInformatics 2013.08. れ
Contents Sequence Homology Analysis ( 覿) 蠍磯蓋 る Gibbs sampling 伎 multiple alignment Sequence Homology Analysis 危 HMMs襯 伎 pairwise sequence alignment 覦伎 一危 郁鍵螻 郁規 襦
Protein function 覦煙 蠍磯レ 殊姶 蟲譟一 蟆一 殊姶 蟲譟磯 殊姶蟲譟一 蟆一 讀, 覦煙 殊姶蟲譟(覩碁語 ) 覿 殊姶 蟲譟一 蟯 覲企ゼ 願 企 family 讌 朱 覦煙 蠍磯 覈襯 豢 企, 伎 蠍磯レ 轟 覿覿 蟇磯, 轟 蠍磯レ れ 蠍一ヾ 覦煙螻殊 煙 蟆曙一 伎 焔慨る 蟲譟一 煙 蠍磯レ 郁煙 覲企 朱 伎 煙 襷れ 殊姶 蟲譟郁 襷れ 蠍磯レ 郁煙 企 蟆曙 螳 . 讌襷 讌蠍蟾讌 れ 殊姶 蟲譟郁 蠍 覓語 伎 伎 覈壱 覿 襴
Protein function 覈壱 覿蠍 瑚讌 螻殊 1. 覈壱 企麹 伎 覦覯 2. 覈壱 伎 觜蟲 螻襴讀 3. 蟆郁骸螳 朱 襤一煙 讌 蟆讀 螻殊 覈壱 覿覦覯 Gibbs sampling PROSITE HMM (BLOCKS, PRINTS) concensus sequence(PRODOM)
Gibbs Sampling 伎 Multiple Alignment 蟲 DNA Alignment DNAれ 觜訣 語れ 谿場 朱 DNA伎 觸企 蠍磯蓋朱 N螳 覲(A, C, G, T 4螳讌 手鍵)螳 り 螳 N by N Matrix襯 襷れ 伎 殊 覿覿 谿場企 覦覯 (朱朱 Waterman 螻襴讀) Multiple Alignment 3螳讌 伎 DNA襯 覲企ゼ 谿場企 DNA螳 3螳 伎 れ願蟆 覃 O(n^3) 螻襴讀 螳蟆 豌蟆 蠍 螳 蟲 企 覓語 願屋蠍 覦覯 譴 螳 gibbs sampling Motif DNA, RNA, Protein 覦覲旧朱 讌ъ ( 譟郁) 100% 殊讌 朱 觜訣 覦覲旧伎 DNA Multiple alignment襯 蠍 譴 key
Gibbs Sampling 伎 Multiple Alignment 蟲 Gibbs Sampling Stochastic algorithm Motif襯 覦覯 100% 企旧 谿場伎 讌襷 觜襯願 所 れ DNA 覦覲旧伎 谿場 豌 伎 蟆 襦 豺 螳 覈壱襯 Gibbs Sampling 1) 蟲 Data 1. Multiple DNA / RNA / Protein sequence 2. Motif width 3. The number of Motif 2) Input朱 譯殊伎 DNA / RNA / Protein sequence 螳 豌企れ 覈 % 讌 豸′伎狩 DNA AAGTC / 5螳 讌ъ 伎 A 40%, G, T, C 螳 20%襷 3) 覓伎朱 sequence motif 豺襯 100螳 手鍵螳 譟伎 DNA伎 motif 蠍語願 10企手 る 1~91, 豐 90螳 豺 企豪 蟆曙一 螳 譟伎 4) PSSM(Position Specific Score Matrix)襯 蟲
Gibbs Sampling 伎 Multiple Alignment 蟲 [ PSSM(Position Specific Score Matrix) 蟲 ] 5螳 sequence襯 譴觜 gibbs sampling 伎伎 pssm 蟲 1)-3 The number of Motif = 8襦 れ 3) motif 豺襯 {s1, s2, s3, s4, s5 | 7, 11, 9, 4, 1} 襦 螳 螳 5螳 sequence 覓伎朱 觜螳覿覿 motif 企 譴 覓語レ choosed sequence襦 讌 PSSM 企 れ 襯 れ Seq 2覯 choosed sequence襦 り 螳 Seq 1. GTAAACAATATTTATAGC Seq 2. AAAATTTACCTTAGAAGG Seq 3. CCGTACTGTCAAGCGTGG Seq 4. TGAGTAAACGACGTCCCA Seq 5. TACTTAACACCCTGTCAA Seq 1. GTAAACAATATTTATAGC Seq 2. AAAATTTACCTTAGAAGG Seq 3. CCGTACTGTCAAGCGTGG Seq 4. TGAGTAAACGACGTCCCA Seq 5. TACTTAACACCCTGTCAA
Gibbs Sampling 伎 Multiple Alignment 蟲 Gibbs Sampling Stochastic algorithm 100% 企旧 谿場伎 讌襷 觜襯願 所 れ DNA 覦覲旧伎 谿場 (豌 襯 覿覿 ) Gibbs Sampling 1) 蟲 Data 1. Multiple DNA / RNA / Protein sequence 2. Motif width 3. The number of Motif 2) Input朱 譯殊伎 DNA / RNA / Protein sequence 螳 豌企れ 覈 % 讌 豸′伎狩 DNA AAGTC / 5螳 讌ъ 伎 A 40%, G, T, C 螳 20%襷 3) 覓伎朱 sequence motif 豺襯 100螳 手鍵螳 譟伎 DNA伎 motif 蠍語願 10企手 る 1~91, 豐 90螳 豺 企豪 蟆曙一 螳 譟伎 4) PSSM(Position Specific Score Matrix)襯 蟲 5) PSSM 譯殊伎 蟆郁骸 score 豸′
Gibbs Sampling 伎 Multiple Alignment 蟲 [ PSSM 譯殊伎 蟆郁骸 score 豸′ ] Seq 2. AAAATTTACCTTAGAAGG 0.25 * 0.5 * 0.5 * 0.75 * 0.5 * 0.25 * 0.25 * 0.5 = 0.000732421875 Seq 2 螳 豺 1企襦 蠍一ヾ 豺 { 7, 11, 9, 4, 1} { 7, 1, 9, 4, 1} 襦 覦蠑語 螻殊 豺 螳 伎 覲螳 蟾讌 覦覲牛
motif, pattern, profile, signature, domain Motif : 伎 覲伎ヾ 伎 覿覿(conserved blocks of sequences) 覩碁ゼ 螳螻, 蟲譟一 覈 螳 伎姶 蟲譟郁 轟 覈朱 覦一企 企 蟲譟(combination of a few secondary structure with a specific geometric arrangement)襦 覦煙 螻牛旧朱 覦 蟆螻 蠍磯 轟 蟲譟一 Pattern : 覈壱覲企る 所 覩 Profile : れ 蟆郁骸襯 , 企 伎企 蟲譟一 覈壱襦 れ伎 覈語 覩 Signature : 譯朱 PROSITE , 豌 伎 覿覿朱, 覿覿襷朱 覦煙 轟(蟲譟 轟 蠍磯) short diagnostic pattern 覩誤, 覦煙螳 谿場願 family襯 Domain : 轟 蠏 伎(蟲譟一 覩語) 覈壱螳 覈 企伎 襴曙 豌企 朱 朱 螻 蠍磯レ 螳讌 Family : 朱 ろ 蟯螻螳 り 覦煙れ 讌 Pairwise sequence alignment 煙 30% 伎 蟯螻 SuperFamily: 螳 轟 蠏 伎 family螳 蟆 覃, 蟲 覦煙 伎 煙 朱 覈 蟯螻螳 讌 讌襷 襷 螳 譟一朱覿 讌 蟆朱 覦煙れ 讌 詩
Sequence Homology Analysis 危 PROSITE (http://prosite.expasy.org/prosite) 煙 企覿 regular expression 伎 覈壱襯 詞 覦煙 family & 覃語 一危磯伎る, 讌蠍蟾讌 覦讌 覈壱襯 伎 襦 覦煙 family襯 谿場 PROSITE 螳 願 觜蟲, 覈壱 覦蟆 煙 觜るゼ 螻牛 危瑚 襷 譟伎(HMMs襯 覈壱 覿 危碁 襷 )
覦伎 一危 郁鍵螻 郁規 襦 1. 豌 覿 蟇磯 襦 A. Human Genome Project 1993-2003 / 覩瑚記 讌覿 蟲襴暑慨蟇伎 譯朱 / 蟲, 朱蓋, , , 譴蟲 / 瑚 DNA 譟伎 20,000螳 襯 讀覈, 瑚 DNA 30 螳 手鍵伎 蟆一, 一危磯伎ろ, 覿蟲 螳覦 煙 覈襦 B. International HapMap Project 朱蓋, 蟲, 貂, 譴蟲, 伎襴, 覩瑚記 讌れ 豌企ゼ 讌譴 覿 瑚 讌覲 手鍵る 覲企 煙 讀覈螻 豺危襦蠏誤 / HapMap 覲企 蟇願, 讌覲, 豌 語 覦 螳語姶 蟯 れ 所 谿剰 郁規 C. 1,000 Genomes Project 蠏覈 ( 1,200覈) 豌企ゼ 企 豌 覯讌 襦語 / 蟆 覿 牛 瑚 覲 手鍵る 覩誤 覲 襯 谿城 襦 / 2010-2011 蟇語 豐 2,500 覲 覲企ゼ 螻 D. International Human Epigenome Consortium(IHEC) 煙豌伎郁規 / 瑚 誤 , 覿 螻襷 1,000螳 伎 谿語＾ 煙豌企ゼ 襷 蟆 / 瑚 讌覲 燕 覃貉る讀 郁規 覦 襷 襦語 E. ENCyclopedia of DNA Elements(ENCODE) 手鍵伎 蠍磯 覦 螳 譟一語 蠏覈 / , 襦覈, 覦 譟一 語, 譟一 語, methylation 覿 れ 覦螻殊 蟯 覿 蠍一 る 覲企ゼ 至鍵 郁規 F. Beijing Genome Institute(BGI) 1999 る / 瑚 3 豌 覿 蠍郁(覩瑚記 Broad Institute, 蟲 Sanger Sequencing Center) / 襷 襦 煙豌器豌企ゼ 一企, 豌 危, DNA 覲伎語 覦 レ 譯朱 語 郁規
覦伎 一危 郁鍵螻 郁規 襦 2. 豌 覿蠍一 A. Whole-Genome Seq 覈豌願 螳讌螻 豌伎 豌 DNA 伎 蟆一 蠍一 / 襦 るジ 螳豌企り 螳豌危轟伎 覲, 讌 轟伎 覲企ゼ 谿 襷れ / reference 一危郁 覓 譬 蟆曙 豌 豐讌 煙 WGS蠍一 一 B. RNA-Seq 蠍一ヾ 襷危襦企 蠍一 豸′ 誤 expression level 豸′ 蟆 襦 蠍一 / 豌 豌 (transcriptome) 豸′ 蟆螻 蟲譟一 覿 螳ロ / 誤 誤 螳 覦 谿願 襯 螻 伎 豺襭覯 郁規 蟆 覦 讌螻 C. Exome-Seq れ 讌覲 襯 覦蟲危 / 讌 exon 蟆一 一危磯れ 蠍 覓語 讌覲 語 蟲讌 蟇磯 るジ variation 煙 蠍一誤 蟆曙 襦 谿 企伎 覈詩 D. ChIP-Seq Chromatin Immunoprecipitation / DNA 覦煙 螳 語 覿蠍 轟 覦煙螻 binding DNA 伎 蠍 / antibody襯 牛 蟯 覦煙螻 覓朱Μ朱 郁屋 轟 DNA豺 ChIP ろ 覿襴 / 企ゼ 誤 覦覯朱 襷危襦企企ゼ 覃 ChIP-chip, NGS 蠍一 伎覃 ChIP-Seq螳 E. FAIRE-Seq Formaldehyde-Assisted Isolation of Regulatory Elements Sequencing / regulatory activity 郁 豌伎 DNA region 覦蠍 / 蠍一ヾ GWAS(Genome-Wide Association Study) 郁規襦 覦伎 覈詩 れ 襷煙 覦 覲牛讌れ 語 覲伎 蠍 煙郁規豌(Epigenetic) 郁規螳 讌 譴 / 覲牛讌 Epigenetic 覲襯 谿場願 覲伎 郁 讌覲 讌 豺襭 豌 郁規 蠍磯 蟲豢 GWAS(Genome-Wide Association Study) = 語 企麹 螳豌伎 DNA 覲企ゼ 燕 , Dna 伎 谿 企ゼ 覿覃 讌覲螻 蟯 DNA 伎 覲企ゼ 詞企企 覦覯
DigSee: Disease gene search engine with evidence sentences(version cancer) 螻 蟯 MEDLINE abstracts 1,391,019 evidence sentences襯 讌 Evidence sentences 豕 gene name(Entrez gene ID螳 覿伎) 螻 螻 event(Turku event extraction system 豢豢)螳 伎 覲 郁規, gene螻 protein 谿剰鍵 ABNER朱 ろ Gene螻 protein Moara襯 伎 normalization
DigSee: Disease gene search engine with evidence sentences(version cancer) Gold-standard data 煙 朱 evidence sentences襯 positive or negative evidence襦 覿襯 Positive : 覓語レ 豢豢 gene 企 event襯 螳螻 螻, 覦 蟯 蟆企朱 覲企ゼ 願 蟆曙 Ex) Significantly, down-regulation of SOX9 by siRNA in prostate cancer cells reduced endogenous AR protein levels, and cell growth indicating that SOX9 contributes to AR regulation and decreased cellular proliferation. Negative: 覓語レ 豢豢 gene 覦 蟯 蟆曙, 轟 豢豢 event螳 gene 轟 cancer 蟯 蟆曙 Ex) To determine the role of CD147 in the invasiveness properties of prostate cancer, we success- fully down- regulated CD147 by RNA interference (RNAi) technology, in PC-3 cell line at high level of CD147 expression. Event types 覦(gene expression), 譟一(regulation), 語壱(phosphorylation), 覦煙 誤 豺 (localization), 覦煙 危(protein catabolism), 覦煙 (binding), (transcription) 覲 伎 豢豢
1. Kim J, So S, Lee H-J, Park JC, Kim J-J, Lee H. DigSee: disease gene search engine with evidence sentences (version cancer). Nucleic acids research. 2013;41(Web Server issue):W5107. 2. 螻蟇危, 蟲讌, 覦煙, 覦蠍一. 豌伎襴 蠍一 襷. 覲願骸讌 2013.8
link 煙豌 http://hongiiv.tistory.com/669 (DNA methylation) http://hongiiv.tistory.com/670 (histone modification) 1,000 genome project http://hongiiv.tistory.com/761 Gibbs Sampling http://celdee.tistory.com/372 http://sosal.tistory.com/432 蟲 Biocomputing 蟆曙 http://biosoft.kisti.re.kr/bcc2011/index.html

More Related Content

2013_08_30_Bioinformatics1_yes

  • 2. Contents Sequence Homology Analysis ( 覿) 蠍磯蓋 る Gibbs sampling 伎 multiple alignment Sequence Homology Analysis 危 HMMs襯 伎 pairwise sequence alignment 覦伎 一危 郁鍵螻 郁規 襦
  • 3. Protein function 覦煙 蠍磯レ 殊姶 蟲譟一 蟆一 殊姶 蟲譟磯 殊姶蟲譟一 蟆一 讀, 覦煙 殊姶蟲譟(覩碁語 ) 覿 殊姶 蟲譟一 蟯 覲企ゼ 願 企 family 讌 朱 覦煙 蠍磯 覈襯 豢 企, 伎 蠍磯レ 轟 覿覿 蟇磯, 轟 蠍磯レ れ 蠍一ヾ 覦煙螻殊 煙 蟆曙一 伎 焔慨る 蟲譟一 煙 蠍磯レ 郁煙 覲企 朱 伎 煙 襷れ 殊姶 蟲譟郁 襷れ 蠍磯レ 郁煙 企 蟆曙 螳 . 讌襷 讌蠍蟾讌 れ 殊姶 蟲譟郁 蠍 覓語 伎 伎 覈壱 覿 襴
  • 4. Protein function 覈壱 覿蠍 瑚讌 螻殊 1. 覈壱 企麹 伎 覦覯 2. 覈壱 伎 觜蟲 螻襴讀 3. 蟆郁骸螳 朱 襤一煙 讌 蟆讀 螻殊 覈壱 覿覦覯 Gibbs sampling PROSITE HMM (BLOCKS, PRINTS) concensus sequence(PRODOM)
  • 5. Gibbs Sampling 伎 Multiple Alignment 蟲 DNA Alignment DNAれ 觜訣 語れ 谿場 朱 DNA伎 觸企 蠍磯蓋朱 N螳 覲(A, C, G, T 4螳讌 手鍵)螳 り 螳 N by N Matrix襯 襷れ 伎 殊 覿覿 谿場企 覦覯 (朱朱 Waterman 螻襴讀) Multiple Alignment 3螳讌 伎 DNA襯 覲企ゼ 谿場企 DNA螳 3螳 伎 れ願蟆 覃 O(n^3) 螻襴讀 螳蟆 豌蟆 蠍 螳 蟲 企 覓語 願屋蠍 覦覯 譴 螳 gibbs sampling Motif DNA, RNA, Protein 覦覲旧朱 讌ъ ( 譟郁) 100% 殊讌 朱 觜訣 覦覲旧伎 DNA Multiple alignment襯 蠍 譴 key
  • 6. Gibbs Sampling 伎 Multiple Alignment 蟲 Gibbs Sampling Stochastic algorithm Motif襯 覦覯 100% 企旧 谿場伎 讌襷 觜襯願 所 れ DNA 覦覲旧伎 谿場 豌 伎 蟆 襦 豺 螳 覈壱襯 Gibbs Sampling 1) 蟲 Data 1. Multiple DNA / RNA / Protein sequence 2. Motif width 3. The number of Motif 2) Input朱 譯殊伎 DNA / RNA / Protein sequence 螳 豌企れ 覈 % 讌 豸′伎狩 DNA AAGTC / 5螳 讌ъ 伎 A 40%, G, T, C 螳 20%襷 3) 覓伎朱 sequence motif 豺襯 100螳 手鍵螳 譟伎 DNA伎 motif 蠍語願 10企手 る 1~91, 豐 90螳 豺 企豪 蟆曙一 螳 譟伎 4) PSSM(Position Specific Score Matrix)襯 蟲
  • 7. Gibbs Sampling 伎 Multiple Alignment 蟲 [ PSSM(Position Specific Score Matrix) 蟲 ] 5螳 sequence襯 譴觜 gibbs sampling 伎伎 pssm 蟲 1)-3 The number of Motif = 8襦 れ 3) motif 豺襯 {s1, s2, s3, s4, s5 | 7, 11, 9, 4, 1} 襦 螳 螳 5螳 sequence 覓伎朱 觜螳覿覿 motif 企 譴 覓語レ choosed sequence襦 讌 PSSM 企 れ 襯 れ Seq 2覯 choosed sequence襦 り 螳 Seq 1. GTAAACAATATTTATAGC Seq 2. AAAATTTACCTTAGAAGG Seq 3. CCGTACTGTCAAGCGTGG Seq 4. TGAGTAAACGACGTCCCA Seq 5. TACTTAACACCCTGTCAA Seq 1. GTAAACAATATTTATAGC Seq 2. AAAATTTACCTTAGAAGG Seq 3. CCGTACTGTCAAGCGTGG Seq 4. TGAGTAAACGACGTCCCA Seq 5. TACTTAACACCCTGTCAA
  • 8. Gibbs Sampling 伎 Multiple Alignment 蟲 Gibbs Sampling Stochastic algorithm 100% 企旧 谿場伎 讌襷 觜襯願 所 れ DNA 覦覲旧伎 谿場 (豌 襯 覿覿 ) Gibbs Sampling 1) 蟲 Data 1. Multiple DNA / RNA / Protein sequence 2. Motif width 3. The number of Motif 2) Input朱 譯殊伎 DNA / RNA / Protein sequence 螳 豌企れ 覈 % 讌 豸′伎狩 DNA AAGTC / 5螳 讌ъ 伎 A 40%, G, T, C 螳 20%襷 3) 覓伎朱 sequence motif 豺襯 100螳 手鍵螳 譟伎 DNA伎 motif 蠍語願 10企手 る 1~91, 豐 90螳 豺 企豪 蟆曙一 螳 譟伎 4) PSSM(Position Specific Score Matrix)襯 蟲 5) PSSM 譯殊伎 蟆郁骸 score 豸′
  • 9. Gibbs Sampling 伎 Multiple Alignment 蟲 [ PSSM 譯殊伎 蟆郁骸 score 豸′ ] Seq 2. AAAATTTACCTTAGAAGG 0.25 * 0.5 * 0.5 * 0.75 * 0.5 * 0.25 * 0.25 * 0.5 = 0.000732421875 Seq 2 螳 豺 1企襦 蠍一ヾ 豺 { 7, 11, 9, 4, 1} { 7, 1, 9, 4, 1} 襦 覦蠑語 螻殊 豺 螳 伎 覲螳 蟾讌 覦覲牛
  • 10. motif, pattern, profile, signature, domain Motif : 伎 覲伎ヾ 伎 覿覿(conserved blocks of sequences) 覩碁ゼ 螳螻, 蟲譟一 覈 螳 伎姶 蟲譟郁 轟 覈朱 覦一企 企 蟲譟(combination of a few secondary structure with a specific geometric arrangement)襦 覦煙 螻牛旧朱 覦 蟆螻 蠍磯 轟 蟲譟一 Pattern : 覈壱覲企る 所 覩 Profile : れ 蟆郁骸襯 , 企 伎企 蟲譟一 覈壱襦 れ伎 覈語 覩 Signature : 譯朱 PROSITE , 豌 伎 覿覿朱, 覿覿襷朱 覦煙 轟(蟲譟 轟 蠍磯) short diagnostic pattern 覩誤, 覦煙螳 谿場願 family襯 Domain : 轟 蠏 伎(蟲譟一 覩語) 覈壱螳 覈 企伎 襴曙 豌企 朱 朱 螻 蠍磯レ 螳讌 Family : 朱 ろ 蟯螻螳 り 覦煙れ 讌 Pairwise sequence alignment 煙 30% 伎 蟯螻 SuperFamily: 螳 轟 蠏 伎 family螳 蟆 覃, 蟲 覦煙 伎 煙 朱 覈 蟯螻螳 讌 讌襷 襷 螳 譟一朱覿 讌 蟆朱 覦煙れ 讌 詩
  • 11. Sequence Homology Analysis 危 PROSITE (http://prosite.expasy.org/prosite) 煙 企覿 regular expression 伎 覈壱襯 詞 覦煙 family & 覃語 一危磯伎る, 讌蠍蟾讌 覦讌 覈壱襯 伎 襦 覦煙 family襯 谿場 PROSITE 螳 願 觜蟲, 覈壱 覦蟆 煙 觜るゼ 螻牛 危瑚 襷 譟伎(HMMs襯 覈壱 覿 危碁 襷 )
  • 12. 覦伎 一危 郁鍵螻 郁規 襦 1. 豌 覿 蟇磯 襦 A. Human Genome Project 1993-2003 / 覩瑚記 讌覿 蟲襴暑慨蟇伎 譯朱 / 蟲, 朱蓋, , , 譴蟲 / 瑚 DNA 譟伎 20,000螳 襯 讀覈, 瑚 DNA 30 螳 手鍵伎 蟆一, 一危磯伎ろ, 覿蟲 螳覦 煙 覈襦 B. International HapMap Project 朱蓋, 蟲, 貂, 譴蟲, 伎襴, 覩瑚記 讌れ 豌企ゼ 讌譴 覿 瑚 讌覲 手鍵る 覲企 煙 讀覈螻 豺危襦蠏誤 / HapMap 覲企 蟇願, 讌覲, 豌 語 覦 螳語姶 蟯 れ 所 谿剰 郁規 C. 1,000 Genomes Project 蠏覈 ( 1,200覈) 豌企ゼ 企 豌 覯讌 襦語 / 蟆 覿 牛 瑚 覲 手鍵る 覩誤 覲 襯 谿城 襦 / 2010-2011 蟇語 豐 2,500 覲 覲企ゼ 螻 D. International Human Epigenome Consortium(IHEC) 煙豌伎郁規 / 瑚 誤 , 覿 螻襷 1,000螳 伎 谿語＾ 煙豌企ゼ 襷 蟆 / 瑚 讌覲 燕 覃貉る讀 郁規 覦 襷 襦語 E. ENCyclopedia of DNA Elements(ENCODE) 手鍵伎 蠍磯 覦 螳 譟一語 蠏覈 / , 襦覈, 覦 譟一 語, 譟一 語, methylation 覿 れ 覦螻殊 蟯 覿 蠍一 る 覲企ゼ 至鍵 郁規 F. Beijing Genome Institute(BGI) 1999 る / 瑚 3 豌 覿 蠍郁(覩瑚記 Broad Institute, 蟲 Sanger Sequencing Center) / 襷 襦 煙豌器豌企ゼ 一企, 豌 危, DNA 覲伎語 覦 レ 譯朱 語 郁規
  • 13. 覦伎 一危 郁鍵螻 郁規 襦 2. 豌 覿蠍一 A. Whole-Genome Seq 覈豌願 螳讌螻 豌伎 豌 DNA 伎 蟆一 蠍一 / 襦 るジ 螳豌企り 螳豌危轟伎 覲, 讌 轟伎 覲企ゼ 谿 襷れ / reference 一危郁 覓 譬 蟆曙 豌 豐讌 煙 WGS蠍一 一 B. RNA-Seq 蠍一ヾ 襷危襦企 蠍一 豸′ 誤 expression level 豸′ 蟆 襦 蠍一 / 豌 豌 (transcriptome) 豸′ 蟆螻 蟲譟一 覿 螳ロ / 誤 誤 螳 覦 谿願 襯 螻 伎 豺襭覯 郁規 蟆 覦 讌螻 C. Exome-Seq れ 讌覲 襯 覦蟲危 / 讌 exon 蟆一 一危磯れ 蠍 覓語 讌覲 語 蟲讌 蟇磯 るジ variation 煙 蠍一誤 蟆曙 襦 谿 企伎 覈詩 D. ChIP-Seq Chromatin Immunoprecipitation / DNA 覦煙 螳 語 覿蠍 轟 覦煙螻 binding DNA 伎 蠍 / antibody襯 牛 蟯 覦煙螻 覓朱Μ朱 郁屋 轟 DNA豺 ChIP ろ 覿襴 / 企ゼ 誤 覦覯朱 襷危襦企企ゼ 覃 ChIP-chip, NGS 蠍一 伎覃 ChIP-Seq螳 E. FAIRE-Seq Formaldehyde-Assisted Isolation of Regulatory Elements Sequencing / regulatory activity 郁 豌伎 DNA region 覦蠍 / 蠍一ヾ GWAS(Genome-Wide Association Study) 郁規襦 覦伎 覈詩 れ 襷煙 覦 覲牛讌れ 語 覲伎 蠍 煙郁規豌(Epigenetic) 郁規螳 讌 譴 / 覲牛讌 Epigenetic 覲襯 谿場願 覲伎 郁 讌覲 讌 豺襭 豌 郁規 蠍磯 蟲豢 GWAS(Genome-Wide Association Study) = 語 企麹 螳豌伎 DNA 覲企ゼ 燕 , Dna 伎 谿 企ゼ 覿覃 讌覲螻 蟯 DNA 伎 覲企ゼ 詞企企 覦覯
  • 14. DigSee: Disease gene search engine with evidence sentences(version cancer) 螻 蟯 MEDLINE abstracts 1,391,019 evidence sentences襯 讌 Evidence sentences 豕 gene name(Entrez gene ID螳 覿伎) 螻 螻 event(Turku event extraction system 豢豢)螳 伎 覲 郁規, gene螻 protein 谿剰鍵 ABNER朱 ろ Gene螻 protein Moara襯 伎 normalization
  • 15. DigSee: Disease gene search engine with evidence sentences(version cancer) Gold-standard data 煙 朱 evidence sentences襯 positive or negative evidence襦 覿襯 Positive : 覓語レ 豢豢 gene 企 event襯 螳螻 螻, 覦 蟯 蟆企朱 覲企ゼ 願 蟆曙 Ex) Significantly, down-regulation of SOX9 by siRNA in prostate cancer cells reduced endogenous AR protein levels, and cell growth indicating that SOX9 contributes to AR regulation and decreased cellular proliferation. Negative: 覓語レ 豢豢 gene 覦 蟯 蟆曙, 轟 豢豢 event螳 gene 轟 cancer 蟯 蟆曙 Ex) To determine the role of CD147 in the invasiveness properties of prostate cancer, we success- fully down- regulated CD147 by RNA interference (RNAi) technology, in PC-3 cell line at high level of CD147 expression. Event types 覦(gene expression), 譟一(regulation), 語壱(phosphorylation), 覦煙 誤 豺 (localization), 覦煙 危(protein catabolism), 覦煙 (binding), (transcription) 覲 伎 豢豢
  • 16. 1. Kim J, So S, Lee H-J, Park JC, Kim J-J, Lee H. DigSee: disease gene search engine with evidence sentences (version cancer). Nucleic acids research. 2013;41(Web Server issue):W5107. 2. 螻蟇危, 蟲讌, 覦煙, 覦蠍一. 豌伎襴 蠍一 襷. 覲願骸讌 2013.8
  • 17. link 煙豌 http://hongiiv.tistory.com/669 (DNA methylation) http://hongiiv.tistory.com/670 (histone modification) 1,000 genome project http://hongiiv.tistory.com/761 Gibbs Sampling http://celdee.tistory.com/372 http://sosal.tistory.com/432 蟲 Biocomputing 蟆曙 http://biosoft.kisti.re.kr/bcc2011/index.html