遺伝子ネットワーク解析
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- たけなり かんけ
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1 I 2 1
2 2
3 23andMe, GeneQuest, MYCODE DNA RNA
4 DNA RNA DNA A, T, G, C RNA or =
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6 BioCyc (EcoCyc) KEGG Reactome WikiPathways TRANSPATH (BIOBASE) Ingenuity Pathway Analysis (IPA) NextBio PathwayStudio -> -> -> Elsevier
7
8 DAVID (Pathways in Cancer, Drug metabolism, ECM receptor interaction )
9
10 BioCyc (EcoCyc) KEGG Reactome WikiPathways TRANSPATH (BIOBASE) Ingenuity Pathway Analysis (IPA) PathwayStudio
11 (PPI: protein-protein interaction) EBI BioGRID IPA BIOBASE, JASPAR, MSigDB GeneMANIA COXPRESdb KEGG, BIOBASE, IPA, PathwayStudio, GeneSpring
12
13 ARACNE: Mutual information BANJO: Bayesian inference CLR: Mutual information MIKANA: Dynamic systems SiGN-BN: Bayesian inference
14 or ARACNE SiGN BIOBASE IPA KEGG GeneSpring PathwayStudio
15
16 1. 16
17 BP -- special.nikkeibp.co.jp/ts/article/aaaa/114314/ Google Facebook Amazon
18 Moneyball: The Art of Winning an Unfair Game 2 March 17, 2004 by Michael Lewis 18
19 20 19
20 2. 20
21 B A 10 B 10 (x, y) = (10, 10) A 20 B 20 (x, y) = (20, 20) A 21
22 (1) B A B A B A B A B A 22
23 (2) B A B A B A B A B A 23
24 20 20 B 10 A A B X Y 24
25 ???
26 A B B C A B C 26
27 A B C A B C A B C 27
28 A B C B A C A B A B C A B C 28
29 A: B: C: A 70% C B 30% 29
30 A B?? C A --> C C --> A 30
31 B --> C --> A A? C B 31
32 B DAG Greedy Hill Climbing BNRC 32
33 3. 33
34 34
35 = Protein-Protein Interaction (PPI) network = = = 35
36 36
37 lincrna 37
38 NCBI Gene Expression Omnibus (GEO) --> Cancer Cell Line Encyclopedia (CCLE) 1000 [GSE36133] The Cancer Genome Atlas (TCGA) SCLS --> 38
39 39
40 logfc 40
41 Affara, M., Dunmore, B., Savoie, C., Imoto, S., Tamada, Y., Araki, H., Charnock-Jones, D. S., et al. (2007). Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal? Philosophical transactions of the Royal Society of London Series B, Biological sciences, 362(1484), doi: /rstb
42 42
43 Gene Network of apoptosis related genes 43
44 ANXA5 (top gene) TP53 (bottom gene) 44
45 ANXA5 TP53 regulating genes TP53 45
46 Big pharma shows signs of renewed interest in RNAi drugs Nature Medicine 20, 109, PCSK9 is the target gene of Alnylam RNAi drug. * Lancet 383, 60-68, 2014.
47 PCSK9 in the gene network PCSK9 exists in the gene network of lipid metabolic process. ( gndb.cell-innovator.com/?page_id=92) 19 children and 3 parents.
48 Next genes of PCSK9? PCSK9 PCSK9? PCSK9 PCSK9 PCSK9 PSCK9 PSCK9 apoptosis
49 Stem Cell Sox2 Oct3/4 Klf4
50 Pou5f1 = Oct3/4 Zscan10 Zscan4a Nanog? Tcl1?
51 Stem Cell GEO BioGPS Oct3/4 180 Sox2 Klf4 Stem Cell SiGN-BN
52 Oct3, Sox2, Klf4 Oct3, Sox2, Klf4 Klf4 Zscan4a 3 Sox2 * Oct3/4 * Jing Jiang et. al., Zscan4 promotes genomic stability during reprogramming and dramatically improves the quality of ips cells as demonstrated by tetraploid complementation. Cell Res. (2012) : 1-15.
53 53
54 XXX 54
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課題名 2 項関係に基づくゲノムと生命システムの機能解読 代表研究者京都大学化学研究所教授金久實 1. 代表研究者による成果概要報告 1-1. 研究開発のねらいヒトからバクテリアまで数多くの生物種において全ゲノム配列が続々と決定され ゲノム情報を基盤に細胞 個体 生態系といった高次生命システムの理解が進み 同時に創薬 医療をはじめとしたゲノム情報の有効利用が活発化している これまでに決定されたゲノムの配列情報は国際
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