細胞周期関連
をテンプレートにして作成
開始行:
[[研究]]
*出芽酵母細胞周期関連遺伝子の制御 [#g9538fef]
**30遺伝子 [#jfb04d31]
|Gene Name|Transcription|Translation|Degradation|Phosphor...
|BUB2||||||
|CDC14||||||
|CDC15||||||
|CDH1|ND|||CDK((localization: S-16,42,176,227,239)), CDC5...
|CLB2|||CDC20,CDH1((&ref_paper(12152084); 25-Dbox,85-,100...
|PDS1|||CDC20, CDH1((8-KEN, 85-Dbox))|CDK((&ref_paper();)...
|CLB5|||CDC20((34-Dbox))|||
|CDC20|||CDH1((tow-Dbox,585-KEN))|||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|SWE1|||CDK,CLA4,CDC5((&ref_paper(15920482);)), HSL1|||
|SWI5|SFF||CDC4((&ref_paper(18787112);))|SRB10((&ref_pape...
|||||||
*その他 [#c532e354]
|Gene Name|Transcription|Translation|Degradation|Phosphor...
|ACM1|MCB, SCB||CDC20, CDH1((&ref_paper(18498748);))|CDK(...
|ALK1|SFF||CDH1?(200-KEN,224-Dbox,[[16855400]])|||
|ALK2|||CDH1?(116-KEN,150-Dbox,[[16855400]])|||
|[[CDC5]]|SFF||CDH1((&ref_paper(11566880);~&ref_paper(181...
|CIN8|HCM1([[16912276]])| | CDH1((&ref_paper(11694576);~ ...
|FIN1| | |CDH1((&ref_paper(17173039);~ 8-Dbox))|CDK((&ref...
|HSL1|MCB, SCB||HOG1((&Ref_paper(16688223);))|CDC20,CDH1(...
|MPS1|||CDC20,CDH1|||
*細胞周期用語集 [#v863e472]
-R-X-X-L-X-X-X-X-[N/D/E] Destruction (D) box APC_Cdc20の...
--[[D-box finder:http://bioinfo.weizmann.ac.il/~danag/d-b...
-K-E-N (KEN box) APC_Cdh1の標的モチーフ((&ref_paper(1073...
-[S/T]-P-X-[K/R] CDKのより厳密なコンセンサス
-[S/T]-P CDKの緩いコンセンサス
-[D/E]-X-[S/T]-Phi-X-[D/E] Polo kinaseのコンセンサス（wh...
-S-[pT/pS]-[P/X] Polo Box binding (PBB) site
-SCF_Cdc4の標的
--Sic1, Swi5
-APC_Cdc20の標的
--Clb5, Clb2, DBF4((&ref_paper(18591250);)),Pds1 (Securin)
-APC_Cdh1の標的
--BUB1((Mammal,&ref_paper(17158872);)),Clb1, Clb2, Cdc5, ...
--A simple database search of budding yeast sequences rev...
-&ref_paper(18591966);~
--The current study verifies previous models of Cdh1 func...
--It is apparent that Cdh1 loss causes genomic instabilit...
#br
**Selected binding sites for cell-cycle transcription fac...
| ||>|Budding yeast|>|Fission yeast|h
|Name |Phase| Binding site*1| TF| Binding site*1| TF|h
|MCB| G1/S| ACGCGT| MBF| ACGCGT| MBF|
|SCB| G1/S| CRCGAAA*2| SBF| Not described| Not described|
|SFF/Forkhead| G2/M| Mcm1*3 + GTAAACAA*2 |Mcm1 + Fkh2 |GT...
|PCB| G2/M| Not described| Not described| GNAACR| PBF, Mb...
|ECB| M/G1| YAATTA + Mcm1*3| Yox1/Yhp1 + Mcm1| Not descri...
|Swi5/Ace2| M/G1| ACCAGCR*2| Swi5, Ace2| ACCAGCCNT*2| Ace2|
+Different versions of binding sites have been described,...
+These sites are also present in reverse orientation.
+A typical Mcm1 site is: TTWCCYAAWNNGGWAA.
N is any base; R is A or G; Y is C or T;Wis A or T.
&ref_paper(16285853);
*細胞周期で制御されている遺伝子はいくつあるのか？ [#s1d48...
これの答えは意外に難しい。
**制御の方法は？ [#jb84ce7b]
+転写
+翻訳
+リン酸化
+分解
**調べる方法は？ [#q12251d1]
-マイクロアレイ解析
-ChIP-chip解析
-ゲノム塩基配列から保存された配列を抽出
-プロテオーム解析
**細胞周期を同調させる方法は？ [#u985029a]
+Induced synchrony, which forces cells to synchronize by ...
+Selection synchrony, which selects a cohort of cells at ...
+Yeasat Metabolic Cycle (YMC) synchrony, which is a natur...
#br
*どんな制御因子があるのか？ [#i9e1c7db]
+転写制御
--SWI4
--SWI6
--MBP1
--HCM1
--MCM1
--FKH2
--NDD1
--SWI5
+リン酸化制御
#br
*[[マイクロアレイ解析]]によるゲノムワイドな細胞周期転写制...
**マイクロアレイによる細胞周期によって制御される転写産物...
-&ref_paper(9702192);~
ゲノムワイドなマイクロアレイと温度感受性変異による同調を...
-&ref_paper(9843569);~
上の論文とやっていることは同じなのだが、クラスタリングや...
#br
----
**最近の解析結果 [#gc7fc1b5]
-&ref_paper(17827275);~
--酵母の代謝周期（Yeast Metabolic Cycle:YMC）によって同調...
--同定できたCCRT（Rowicka's CCRT）は、1,129個！
#br
#ref(http://www.pnas.org/content/104/43/16892/F4.large.jp...
#br
----
-&ref_paper(18463633);
-&ref_paper(18758238);
--clb1,2,3,4,5,6, GAL-CLB1株を用いてサイクリンの発現を止...
データを見ると、振動してはいない。順番に転写活性化が起き...
#br
#ref(http://www.nature.com/nature/journal/v453/n7197/imag...
#br
----
-[[細胞周期で制御を受ける遺伝子データベース:http://www.cy...
割と見やすくてよいが、上記の論文のデータがアップデートさ...
#br
*出芽酵母のゲノムを細胞周期制御モチーフからみる [#n214e3b8]
SGDの[[Pattern Matching:http://seq.yeastgenome.org/cgi-bi...
|Motif | Unique hit| Total hit |h
|KEN box (KEN) | 871 | 1025 |
|D-box (RxxLxxxx[DEN]) | 1686 | 2246 |
|D-box (RxxLxxxx[DENQ])| 1951 | 2741 |
|CDK ([ST]Px[KR]) | 1440 | 2108 |
|Moc1 (LFP) | 498 | 529 |
|Moc2 ([ST]Pxx[KR]) | 1639 | 2254 |
|Total ORF | 5884 | |
#br
Mocにあるように適当な配列を用いて検索をかけても、多くの蛋...
#br
| Name | CCRT | CDK | D_hit | KEN |h
| ACC1 | G1 | 4 | 1 | 1 |
| AFR1 | M | 1 | 1 | 1 |
| ALK1* | G2 | 1 | 1 | 1 |
| ALK2* | S | 2 | 1 | 1 |
| ATF1 | G2/M | 1 | 1 | 1 |
| BFR1 | S | 1 | 1 | 1 |
| BNR1 | G1/S | 2 | 1 | 1 |
| BUD3 | G2 | 5 | 2 | 1 |
| CDC20* | M | 1 | 1 | 1 |
| CDC5* | G2 | 1 | 2 | 1 |
| CSR1 | G1(P) | 1 | 1 | 1 |
| ERM6 | G2 | 1 | 1 | 1 |
| FAA3 | G2/M | 1 | 1 | 1 |
| FKH2 | G1(P) | 3 | 1 | 1 |
| GPT2 | G2/M | 1 | 1 | 1 |
| HPC2 | S | 4 | 1 | 1 |
| HSL1* | S | 2 | 4 | 3 |
| IQG1* | M | 4 | 3 | 2 |
| ISW1 | G1(P) | 1 | 3 | 3 |
| KAR3 | S | 2 | 2 | 1 |
| KEL1 | S | 2 | 1 | 2 |
| KEL2 | G1/S | 1 | 1 | 1 |
| KIP1 | S | 1 | 1 | 1 |
| LTE1 | G1(P) | 8 | 1 | 1 |
| MMS4 | G1/S | 3 | 1 | 1 |
| MPS1* | M | 1 | 1 | 1 |
| MSC7 | G1(P) | 1 | 1 | 1 |
| MYO2 | S | 1 | 1 | 1 |
| NTE1 | S | 1 | 1 | 1 |
| NUM1 | G1 | 2 | 2 | 13 |
| PDS1* | S | 3 | 1 | 1 |
| SGS1 | S | 1 | 1 | 2 |
| SIR4 | G2 | 5 | 1 | 1 |
| SKM1 | G1/S | 1 | 1 | 1 |
| SPC72 | G1 | 1 | 1 | 1 |
| SPT16 | M/G1 | 1 | 1 | 2 |
| STH1 | S | 1 | 1 | 3 |
| STU1 | G1/S | 1 | 1 | 1 |
| STU2 | S | 1 | 1 | 1 |
| SUM1 | G1(P) | 1 | 1 | 1 |
| SVL3 | S | 1 | 2 | 1 |
| SWI4 | M | 2 | 1 | 1 |
| SWI5 | G2/M | 8 | 1 | 1 |
| TOS2 | G1/S | 1 | 1 | 1 |
| TRA1 | G1(P) | 4 | 5 | 4 |
| UBP7 | G1 | 1 | 3 | 1 |
| ULS1 | M/G1 | 2 | 1 | 2 |
| VAC17 | G2 | 2 | 1 | 1 |
| YCS4 | S | 1 | 1 | 1 |
| YHP1 | S | 2 | 1 | 1 |
| YLR057W | G1(P) | 1 | 1 | 1 |
CENTER: *CDH1のターゲットであることがわかっている遺伝子。
*Morgan's CDK substrate [#u7fe32c5]
| Protein | Clb5/Clb2 | Biological Process |h
| Ace2 | 1.3 | Required for G1-specific transcription |
| Ady3 | 3.4 | Protein of unknown function |
| Arg1 | 0.7 | Argininosuccinate synthetase |
| Ase1 | 15.8 | Microtubule binding protein required for ...
| Ash1 | 1.7 | Daughter cell-localized transcription fact...
| Atg20 | 0.5 | Protein of unknown function |
| Axl2 | 2.0 | Required for axial budding pattern |
| Bbp1 | 3.1 | Spindle pole body component |
| Bck2 | 0.4 | Protein involved in the SIT4 pathway for C...
| Bem1 | 0.9 | Required for cell polarization and bud for...
| Bem3 | 1.5 | GTPase-activating protein Cdc42p and Rho1p |
| Bna3 | 1.7 | Arylformamidase |
| Bni1 | 4.3 | Involved in cytoskeletal control |
| Bsp1 | 2.2 | Organization of actin cytoskeleton |
| Bud4 | 0.4 | Required for axial budding |
| Bud6 | 0.4 | Required for bipolar budding |
| Caf120 | 1.2 | Transcriptional regulation |
| Cdc20 | 2.3 | APC-activating factor in anaphase |
| Cdc5 | 1.1 | Protein kinase required for mitotic exit |
| Cdc6 | 758.6 | pre-replicative complex formation and ma...
| Cdh1 | 5.6 | APC activating factor in M/G1 |
| Chs2 | 0.4 | Responsible for primary septum disk during...
| Cnn1 | 45.7 | Protein of unknown function |
| Csr2 | 0.6 | Protein of unknown function |
| Cst9 | 1.4 | Required for synaptonemal complex formatio...
| Cyc2 | 0.8 | Cytochrome-c mitochondrial import factor |
| Dbf2 | 2.2 | Protein kinase required for mitotic exit |
| Dbf20 | 2.4 | Protein kinase required for mitotic exit |
| Dbf4 | 1.9 | Regulatory subunit for Cdc7p protein kinas...
| Ddc1 | 13.1 | DNA damage checkpoint protein |
| Dna2 | 0.6 | DNA helicase |
| Dna43 | 1.5 | DNA replication initiation / DNA strand e...
| Dnf2 | 1.2 | Protein of unknown function |
| Dpb2 | 10.5 | DNA polymerase epsilon subunit |
| Eco1 | 2.5 | Required for establishment of sister chrom...
| Elm1 | 0.7 | Protein kinase regulating pseudohyphal gro...
| Far1 | 3.3 | Cln-specific Cdk1 inhibitor |
| Fin1 | 13.8 | Intermediate filament protein |
| Fkh2 | 3.5 | Transcription factor regulating G2/M gene ...
| Fmt1 | 1.6 | Mitochondrial methionyl-tRNA transformylas...
| Frt2 | 20.3 | ER protein of unknown function |
| Fun21 | 0.7 | Protein of unknown function |
| Fun30 | 0.9 | Involved in resistance to UV radiation |
| Fus1 | 3.0 | Required for cell fusion during mating |
| Gin4 | 1.9 | Protein kinase required for septin organiz...
| Hcm1 | 2.0 | Member of the forkhead family of DNA-bindi...
| Hdr1 | 0.8 | Protein involved in meiotic segregation |
| Hos4 | 1.0 | Protein of unknown function |
| Icy2 | 0.8 | Protein of unknown function |
| Ifh1 | 0.9 | Involved in regulation of ribosomal RNA ex...
| Ino2 | 1.3 | Transcription factor required for derepres...
| Ipl1 | 1.8 | Protein kinase involved in chromosome segr...
| Jsn1 | 1.7 | RNA-binding protein |
| Kar3 | 5.9 | Kinesin-like protein required for proper s...
| Kar9 | 4.8 | Involved in mitotic spindle orientation |
| Kel1 | 5.1 | Involved in cell fusion and morphology |
| Kel2 | 0.4 | Protein involved in cell fusion and morpho...
| Kip2 | 0.7 | Kinesin-like protein required for proper s...
| Kip3 | 2.1 | Kinesin-like protein required for proper s...
| Lre1 | 1.5 | Protein of unknown function |
| Lrs4 | 2.5 | Involved in rDNA silencing |
| Lte1 | 0.3 | GDP exchange factor involved in mitotic ex...
| Luv1 | 1.6 | Involved in protein sorting in the late Go...
| Mcm2 | 0.8 | Subunit of MCM complex at origins of DNA r...
| Mcm3 | 16.2 | Subunit of MCM complex at origins of DNA ...
| Mcm6 | 0.7 | Subunit of MCM complex at origins of DNA r...
| Mih1 | 6.1 | Phosphatase that dephosphorylates Y19 on C...
| Mlp1 | 0.7 | Myosin-like protein |
| Mmr1 | 2.3 | Protein of unknown function |
| Mms4 | 0.8 | DNA damage repair protein |
| Mob1 | 0.8 | Regulatory subunit of Dbf2, required for m...
| Mpc54 | 2.0 | Component of the meiotic plaque |
| Mps2 | 18.3 | Required for spindle pole body assembly a...
| Mpt1 | 1.4 | Component of RNA polymerase II transcripti...
| Msb1 | 1.5 | Required for establishment of cell polarit...
| Msh6 | 1.0 | DNA repair protein |
| Nbp1 | 1.7 | Essential protein required for G2/M transi...
| Ndd1 | 2.6 | Interacts with Fkh2 to control G2/M gene e...
| Net1 | 0.4 | Control of the Cdc14 phosphatase |
| Nth1 | 3.6 | Neutral trehalase |
| Nup1 | 0.9 | Nuclear pore protein (nucleoporin) |
| Nup60 | 2.7 | Nuclear pore protein (nucleoporin) |
| Orc1 | 2.4 | Required in pre-replicative complex format...
| Orc2 | 26.9 | Required in pre-replicative complex forma...
| Orc6 | 67.9 | Required in pre-replicative complex forma...
| Pak1 | 1.7 | Kinase that suppresses DNA pol. alpha muta...
| Pcl7 | 1.0 | Pho85 cyclin |
| Pin2 | 1.2 | Protein of unknown function |
| Pkh2 | 1.2 | protein kinase with similarity to 3-phosph...
| Plm2 | 1.5 | Required for plasmid maintenance |
| Pol1 | 1.0 | DNA polymerase I alpha subunit |
| Pom152 | 1.0 | Nuclear pore membrane glycoprotein |
| Ptk2 | 0.6 | Protein kinase required for polyamine tran...
| Pxl1 | 0.9 | Involved in polarized growth |
| Rad9 | 0.5 | DNA damage checkpoint protein |
| Rav1 | 1.9 | Involved in regulation of (H+)-ATPase in v...
| Rbs1 | 1.3 | Protein of unknown function |
| Rfc1 | 0.4 | Subunit of RFC complex required for DNA re...
| Rlf2 | 1.1 | Involved in nucleosome assembly |
| Rrp6 | 1.7 | Involved in 5.8S ribosomal RNA 3' end proc...
| Rts1 | 2.0 | PP2A regulatory subunit |
| Sac7 | 1.3 | GTPase-activating protein for Rho1p |
| Sec3 | 1.7 | Component of exocyst complex |
| Sfb3 | 0.9 | Involved in transport of protein from the ...
| Sld2 | 14.2 | Required for initiation of DNA replicatio...
| Sld3 | 2.1 | Involved in initiation of DNA replication |
| Slk19 | 1.8 | Kinetochore protein required for spindle ...
| Smc4 | 2.7 | Subunit of the condensin protein complex |
| Spa2 | 0.8 | Involved in cell polarity and cell fusion ...
| Spc110 | 54.2 | Spindle pole body component |
| Src1 | 0.2 | Protein of unknown function |
| Srm1 | 1.5 | GDP/GTP exchange factor for Gsp1p and Gsp2...
| Ssk1 | 0.6 | Involved in osmosensory signal transductio...
| Stb1 | 2.5 | Involved in transcription regulation at St...
| Stu2 | 0.9 | SPB component regulatin microtubule dynami...
| Swe1 | 1.7 | Protein kinase that phosphorylates Cdk1 on...
| Swi5 | 2.4 | G1-specific transcription factor |
| Swi6 | 1.0 | G1-specific transcription factor |
| Tfg1 | 3.3 | RNA polymerase II transcription initiation...
| Tus1 | 0.6 | Protein with similarity to GDP-GTP exchang...
| Ufe1 | 1.3 | t-SNARE homolog of the endoplasmic reticul...
| Ulp2 | 5.3 | Degrades conjugated ubiquitin-like protein...
| Whi5 | 1.6 | Regulation of progression through Start |
| Xbp1 | 1.9 | Stress-induced transcriptional repressor |
| YDL025C | 0.9 | Protein kinase of unknown function |
| YDL089W | 0.6 | Protein of unknown function |
| YDR348C | 1.8 | Protein of unknown function |
| Yen1 | 364.4 | Protein of unknown function |
| YER158C | 1.2 | Protein of unknown function |
| YGR035C | 0.5 | Protein of unknown function |
| YHL035C | 1.2 | Protein of unknown function |
| YHR149C | 1.0 | Protein of unknown function |
| YJL084C | 1.3 | Protein of unknown function |
| YJR054W | 4.8 | Protein of unknown function |
| YKR078W | 0.3 | Protein of unknown function |
| YLR187W | 1.5 | Protein of unknown function |
| YLR278C | 0.9 | Protein of unknown function |
| YML119W | 0.5 | Protein of unknown function |
| YNL058C | 1.2 | Protein of unknown function |
| YNL321W | 3.1 | Member of the calcium permease family o...
| YNR047W | 4.3 | Protein kinase of unknown function |
| YOL036W | 2.6 | Protein of unknown function |
| YOL070C | 0.6 | Protein of unknown function |
| YOR066W | 1.9 | Protein of unknown function |
| YOR315W | 0.5 | Protein of unknown function |
| YPL267W | 1.6 | Protein of unknown function |
| Yrf1-3 | 1.4 | Protein of unknown function |
| Yrf1-6 | 0.7 | Protein of unknown function |
| Yta7 | 1.4 | Protein of unknown function |
| Zip1 | 3.4 | Structural protein of the synaptonemal com...
[[FrontPage]]
RIGHT:&lastmod();
終了行:
[[研究]]
*出芽酵母細胞周期関連遺伝子の制御 [#g9538fef]
**30遺伝子 [#jfb04d31]
|Gene Name|Transcription|Translation|Degradation|Phosphor...
|BUB2||||||
|CDC14||||||
|CDC15||||||
|CDH1|ND|||CDK((localization: S-16,42,176,227,239)), CDC5...
|CLB2|||CDC20,CDH1((&ref_paper(12152084); 25-Dbox,85-,100...
|PDS1|||CDC20, CDH1((8-KEN, 85-Dbox))|CDK((&ref_paper();)...
|CLB5|||CDC20((34-Dbox))|||
|CDC20|||CDH1((tow-Dbox,585-KEN))|||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|||||||
|SWE1|||CDK,CLA4,CDC5((&ref_paper(15920482);)), HSL1|||
|SWI5|SFF||CDC4((&ref_paper(18787112);))|SRB10((&ref_pape...
|||||||
*その他 [#c532e354]
|Gene Name|Transcription|Translation|Degradation|Phosphor...
|ACM1|MCB, SCB||CDC20, CDH1((&ref_paper(18498748);))|CDK(...
|ALK1|SFF||CDH1?(200-KEN,224-Dbox,[[16855400]])|||
|ALK2|||CDH1?(116-KEN,150-Dbox,[[16855400]])|||
|[[CDC5]]|SFF||CDH1((&ref_paper(11566880);~&ref_paper(181...
|CIN8|HCM1([[16912276]])| | CDH1((&ref_paper(11694576);~ ...
|FIN1| | |CDH1((&ref_paper(17173039);~ 8-Dbox))|CDK((&ref...
|HSL1|MCB, SCB||HOG1((&Ref_paper(16688223);))|CDC20,CDH1(...
|MPS1|||CDC20,CDH1|||
*細胞周期用語集 [#v863e472]
-R-X-X-L-X-X-X-X-[N/D/E] Destruction (D) box APC_Cdc20の...
--[[D-box finder:http://bioinfo.weizmann.ac.il/~danag/d-b...
-K-E-N (KEN box) APC_Cdh1の標的モチーフ((&ref_paper(1073...
-[S/T]-P-X-[K/R] CDKのより厳密なコンセンサス
-[S/T]-P CDKの緩いコンセンサス
-[D/E]-X-[S/T]-Phi-X-[D/E] Polo kinaseのコンセンサス（wh...
-S-[pT/pS]-[P/X] Polo Box binding (PBB) site
-SCF_Cdc4の標的
--Sic1, Swi5
-APC_Cdc20の標的
--Clb5, Clb2, DBF4((&ref_paper(18591250);)),Pds1 (Securin)
-APC_Cdh1の標的
--BUB1((Mammal,&ref_paper(17158872);)),Clb1, Clb2, Cdc5, ...
--A simple database search of budding yeast sequences rev...
-&ref_paper(18591966);~
--The current study verifies previous models of Cdh1 func...
--It is apparent that Cdh1 loss causes genomic instabilit...
#br
**Selected binding sites for cell-cycle transcription fac...
| ||>|Budding yeast|>|Fission yeast|h
|Name |Phase| Binding site*1| TF| Binding site*1| TF|h
|MCB| G1/S| ACGCGT| MBF| ACGCGT| MBF|
|SCB| G1/S| CRCGAAA*2| SBF| Not described| Not described|
|SFF/Forkhead| G2/M| Mcm1*3 + GTAAACAA*2 |Mcm1 + Fkh2 |GT...
|PCB| G2/M| Not described| Not described| GNAACR| PBF, Mb...
|ECB| M/G1| YAATTA + Mcm1*3| Yox1/Yhp1 + Mcm1| Not descri...
|Swi5/Ace2| M/G1| ACCAGCR*2| Swi5, Ace2| ACCAGCCNT*2| Ace2|
+Different versions of binding sites have been described,...
+These sites are also present in reverse orientation.
+A typical Mcm1 site is: TTWCCYAAWNNGGWAA.
N is any base; R is A or G; Y is C or T;Wis A or T.
&ref_paper(16285853);
*細胞周期で制御されている遺伝子はいくつあるのか？ [#s1d48...
これの答えは意外に難しい。
**制御の方法は？ [#jb84ce7b]
+転写
+翻訳
+リン酸化
+分解
**調べる方法は？ [#q12251d1]
-マイクロアレイ解析
-ChIP-chip解析
-ゲノム塩基配列から保存された配列を抽出
-プロテオーム解析
**細胞周期を同調させる方法は？ [#u985029a]
+Induced synchrony, which forces cells to synchronize by ...
+Selection synchrony, which selects a cohort of cells at ...
+Yeasat Metabolic Cycle (YMC) synchrony, which is a natur...
#br
*どんな制御因子があるのか？ [#i9e1c7db]
+転写制御
--SWI4
--SWI6
--MBP1
--HCM1
--MCM1
--FKH2
--NDD1
--SWI5
+リン酸化制御
#br
*[[マイクロアレイ解析]]によるゲノムワイドな細胞周期転写制...
**マイクロアレイによる細胞周期によって制御される転写産物...
-&ref_paper(9702192);~
ゲノムワイドなマイクロアレイと温度感受性変異による同調を...
-&ref_paper(9843569);~
上の論文とやっていることは同じなのだが、クラスタリングや...
#br
----
**最近の解析結果 [#gc7fc1b5]
-&ref_paper(17827275);~
--酵母の代謝周期（Yeast Metabolic Cycle:YMC）によって同調...
--同定できたCCRT（Rowicka's CCRT）は、1,129個！
#br
#ref(http://www.pnas.org/content/104/43/16892/F4.large.jp...
#br
----
-&ref_paper(18463633);
-&ref_paper(18758238);
--clb1,2,3,4,5,6, GAL-CLB1株を用いてサイクリンの発現を止...
データを見ると、振動してはいない。順番に転写活性化が起き...
#br
#ref(http://www.nature.com/nature/journal/v453/n7197/imag...
#br
----
-[[細胞周期で制御を受ける遺伝子データベース:http://www.cy...
割と見やすくてよいが、上記の論文のデータがアップデートさ...
#br
*出芽酵母のゲノムを細胞周期制御モチーフからみる [#n214e3b8]
SGDの[[Pattern Matching:http://seq.yeastgenome.org/cgi-bi...
|Motif | Unique hit| Total hit |h
|KEN box (KEN) | 871 | 1025 |
|D-box (RxxLxxxx[DEN]) | 1686 | 2246 |
|D-box (RxxLxxxx[DENQ])| 1951 | 2741 |
|CDK ([ST]Px[KR]) | 1440 | 2108 |
|Moc1 (LFP) | 498 | 529 |
|Moc2 ([ST]Pxx[KR]) | 1639 | 2254 |
|Total ORF | 5884 | |
#br
Mocにあるように適当な配列を用いて検索をかけても、多くの蛋...
#br
| Name | CCRT | CDK | D_hit | KEN |h
| ACC1 | G1 | 4 | 1 | 1 |
| AFR1 | M | 1 | 1 | 1 |
| ALK1* | G2 | 1 | 1 | 1 |
| ALK2* | S | 2 | 1 | 1 |
| ATF1 | G2/M | 1 | 1 | 1 |
| BFR1 | S | 1 | 1 | 1 |
| BNR1 | G1/S | 2 | 1 | 1 |
| BUD3 | G2 | 5 | 2 | 1 |
| CDC20* | M | 1 | 1 | 1 |
| CDC5* | G2 | 1 | 2 | 1 |
| CSR1 | G1(P) | 1 | 1 | 1 |
| ERM6 | G2 | 1 | 1 | 1 |
| FAA3 | G2/M | 1 | 1 | 1 |
| FKH2 | G1(P) | 3 | 1 | 1 |
| GPT2 | G2/M | 1 | 1 | 1 |
| HPC2 | S | 4 | 1 | 1 |
| HSL1* | S | 2 | 4 | 3 |
| IQG1* | M | 4 | 3 | 2 |
| ISW1 | G1(P) | 1 | 3 | 3 |
| KAR3 | S | 2 | 2 | 1 |
| KEL1 | S | 2 | 1 | 2 |
| KEL2 | G1/S | 1 | 1 | 1 |
| KIP1 | S | 1 | 1 | 1 |
| LTE1 | G1(P) | 8 | 1 | 1 |
| MMS4 | G1/S | 3 | 1 | 1 |
| MPS1* | M | 1 | 1 | 1 |
| MSC7 | G1(P) | 1 | 1 | 1 |
| MYO2 | S | 1 | 1 | 1 |
| NTE1 | S | 1 | 1 | 1 |
| NUM1 | G1 | 2 | 2 | 13 |
| PDS1* | S | 3 | 1 | 1 |
| SGS1 | S | 1 | 1 | 2 |
| SIR4 | G2 | 5 | 1 | 1 |
| SKM1 | G1/S | 1 | 1 | 1 |
| SPC72 | G1 | 1 | 1 | 1 |
| SPT16 | M/G1 | 1 | 1 | 2 |
| STH1 | S | 1 | 1 | 3 |
| STU1 | G1/S | 1 | 1 | 1 |
| STU2 | S | 1 | 1 | 1 |
| SUM1 | G1(P) | 1 | 1 | 1 |
| SVL3 | S | 1 | 2 | 1 |
| SWI4 | M | 2 | 1 | 1 |
| SWI5 | G2/M | 8 | 1 | 1 |
| TOS2 | G1/S | 1 | 1 | 1 |
| TRA1 | G1(P) | 4 | 5 | 4 |
| UBP7 | G1 | 1 | 3 | 1 |
| ULS1 | M/G1 | 2 | 1 | 2 |
| VAC17 | G2 | 2 | 1 | 1 |
| YCS4 | S | 1 | 1 | 1 |
| YHP1 | S | 2 | 1 | 1 |
| YLR057W | G1(P) | 1 | 1 | 1 |
CENTER: *CDH1のターゲットであることがわかっている遺伝子。
*Morgan's CDK substrate [#u7fe32c5]
| Protein | Clb5/Clb2 | Biological Process |h
| Ace2 | 1.3 | Required for G1-specific transcription |
| Ady3 | 3.4 | Protein of unknown function |
| Arg1 | 0.7 | Argininosuccinate synthetase |
| Ase1 | 15.8 | Microtubule binding protein required for ...
| Ash1 | 1.7 | Daughter cell-localized transcription fact...
| Atg20 | 0.5 | Protein of unknown function |
| Axl2 | 2.0 | Required for axial budding pattern |
| Bbp1 | 3.1 | Spindle pole body component |
| Bck2 | 0.4 | Protein involved in the SIT4 pathway for C...
| Bem1 | 0.9 | Required for cell polarization and bud for...
| Bem3 | 1.5 | GTPase-activating protein Cdc42p and Rho1p |
| Bna3 | 1.7 | Arylformamidase |
| Bni1 | 4.3 | Involved in cytoskeletal control |
| Bsp1 | 2.2 | Organization of actin cytoskeleton |
| Bud4 | 0.4 | Required for axial budding |
| Bud6 | 0.4 | Required for bipolar budding |
| Caf120 | 1.2 | Transcriptional regulation |
| Cdc20 | 2.3 | APC-activating factor in anaphase |
| Cdc5 | 1.1 | Protein kinase required for mitotic exit |
| Cdc6 | 758.6 | pre-replicative complex formation and ma...
| Cdh1 | 5.6 | APC activating factor in M/G1 |
| Chs2 | 0.4 | Responsible for primary septum disk during...
| Cnn1 | 45.7 | Protein of unknown function |
| Csr2 | 0.6 | Protein of unknown function |
| Cst9 | 1.4 | Required for synaptonemal complex formatio...
| Cyc2 | 0.8 | Cytochrome-c mitochondrial import factor |
| Dbf2 | 2.2 | Protein kinase required for mitotic exit |
| Dbf20 | 2.4 | Protein kinase required for mitotic exit |
| Dbf4 | 1.9 | Regulatory subunit for Cdc7p protein kinas...
| Ddc1 | 13.1 | DNA damage checkpoint protein |
| Dna2 | 0.6 | DNA helicase |
| Dna43 | 1.5 | DNA replication initiation / DNA strand e...
| Dnf2 | 1.2 | Protein of unknown function |
| Dpb2 | 10.5 | DNA polymerase epsilon subunit |
| Eco1 | 2.5 | Required for establishment of sister chrom...
| Elm1 | 0.7 | Protein kinase regulating pseudohyphal gro...
| Far1 | 3.3 | Cln-specific Cdk1 inhibitor |
| Fin1 | 13.8 | Intermediate filament protein |
| Fkh2 | 3.5 | Transcription factor regulating G2/M gene ...
| Fmt1 | 1.6 | Mitochondrial methionyl-tRNA transformylas...
| Frt2 | 20.3 | ER protein of unknown function |
| Fun21 | 0.7 | Protein of unknown function |
| Fun30 | 0.9 | Involved in resistance to UV radiation |
| Fus1 | 3.0 | Required for cell fusion during mating |
| Gin4 | 1.9 | Protein kinase required for septin organiz...
| Hcm1 | 2.0 | Member of the forkhead family of DNA-bindi...
| Hdr1 | 0.8 | Protein involved in meiotic segregation |
| Hos4 | 1.0 | Protein of unknown function |
| Icy2 | 0.8 | Protein of unknown function |
| Ifh1 | 0.9 | Involved in regulation of ribosomal RNA ex...
| Ino2 | 1.3 | Transcription factor required for derepres...
| Ipl1 | 1.8 | Protein kinase involved in chromosome segr...
| Jsn1 | 1.7 | RNA-binding protein |
| Kar3 | 5.9 | Kinesin-like protein required for proper s...
| Kar9 | 4.8 | Involved in mitotic spindle orientation |
| Kel1 | 5.1 | Involved in cell fusion and morphology |
| Kel2 | 0.4 | Protein involved in cell fusion and morpho...
| Kip2 | 0.7 | Kinesin-like protein required for proper s...
| Kip3 | 2.1 | Kinesin-like protein required for proper s...
| Lre1 | 1.5 | Protein of unknown function |
| Lrs4 | 2.5 | Involved in rDNA silencing |
| Lte1 | 0.3 | GDP exchange factor involved in mitotic ex...
| Luv1 | 1.6 | Involved in protein sorting in the late Go...
| Mcm2 | 0.8 | Subunit of MCM complex at origins of DNA r...
| Mcm3 | 16.2 | Subunit of MCM complex at origins of DNA ...
| Mcm6 | 0.7 | Subunit of MCM complex at origins of DNA r...
| Mih1 | 6.1 | Phosphatase that dephosphorylates Y19 on C...
| Mlp1 | 0.7 | Myosin-like protein |
| Mmr1 | 2.3 | Protein of unknown function |
| Mms4 | 0.8 | DNA damage repair protein |
| Mob1 | 0.8 | Regulatory subunit of Dbf2, required for m...
| Mpc54 | 2.0 | Component of the meiotic plaque |
| Mps2 | 18.3 | Required for spindle pole body assembly a...
| Mpt1 | 1.4 | Component of RNA polymerase II transcripti...
| Msb1 | 1.5 | Required for establishment of cell polarit...
| Msh6 | 1.0 | DNA repair protein |
| Nbp1 | 1.7 | Essential protein required for G2/M transi...
| Ndd1 | 2.6 | Interacts with Fkh2 to control G2/M gene e...
| Net1 | 0.4 | Control of the Cdc14 phosphatase |
| Nth1 | 3.6 | Neutral trehalase |
| Nup1 | 0.9 | Nuclear pore protein (nucleoporin) |
| Nup60 | 2.7 | Nuclear pore protein (nucleoporin) |
| Orc1 | 2.4 | Required in pre-replicative complex format...
| Orc2 | 26.9 | Required in pre-replicative complex forma...
| Orc6 | 67.9 | Required in pre-replicative complex forma...
| Pak1 | 1.7 | Kinase that suppresses DNA pol. alpha muta...
| Pcl7 | 1.0 | Pho85 cyclin |
| Pin2 | 1.2 | Protein of unknown function |
| Pkh2 | 1.2 | protein kinase with similarity to 3-phosph...
| Plm2 | 1.5 | Required for plasmid maintenance |
| Pol1 | 1.0 | DNA polymerase I alpha subunit |
| Pom152 | 1.0 | Nuclear pore membrane glycoprotein |
| Ptk2 | 0.6 | Protein kinase required for polyamine tran...
| Pxl1 | 0.9 | Involved in polarized growth |
| Rad9 | 0.5 | DNA damage checkpoint protein |
| Rav1 | 1.9 | Involved in regulation of (H+)-ATPase in v...
| Rbs1 | 1.3 | Protein of unknown function |
| Rfc1 | 0.4 | Subunit of RFC complex required for DNA re...
| Rlf2 | 1.1 | Involved in nucleosome assembly |
| Rrp6 | 1.7 | Involved in 5.8S ribosomal RNA 3' end proc...
| Rts1 | 2.0 | PP2A regulatory subunit |
| Sac7 | 1.3 | GTPase-activating protein for Rho1p |
| Sec3 | 1.7 | Component of exocyst complex |
| Sfb3 | 0.9 | Involved in transport of protein from the ...
| Sld2 | 14.2 | Required for initiation of DNA replicatio...
| Sld3 | 2.1 | Involved in initiation of DNA replication |
| Slk19 | 1.8 | Kinetochore protein required for spindle ...
| Smc4 | 2.7 | Subunit of the condensin protein complex |
| Spa2 | 0.8 | Involved in cell polarity and cell fusion ...
| Spc110 | 54.2 | Spindle pole body component |
| Src1 | 0.2 | Protein of unknown function |
| Srm1 | 1.5 | GDP/GTP exchange factor for Gsp1p and Gsp2...
| Ssk1 | 0.6 | Involved in osmosensory signal transductio...
| Stb1 | 2.5 | Involved in transcription regulation at St...
| Stu2 | 0.9 | SPB component regulatin microtubule dynami...
| Swe1 | 1.7 | Protein kinase that phosphorylates Cdk1 on...
| Swi5 | 2.4 | G1-specific transcription factor |
| Swi6 | 1.0 | G1-specific transcription factor |
| Tfg1 | 3.3 | RNA polymerase II transcription initiation...
| Tus1 | 0.6 | Protein with similarity to GDP-GTP exchang...
| Ufe1 | 1.3 | t-SNARE homolog of the endoplasmic reticul...
| Ulp2 | 5.3 | Degrades conjugated ubiquitin-like protein...
| Whi5 | 1.6 | Regulation of progression through Start |
| Xbp1 | 1.9 | Stress-induced transcriptional repressor |
| YDL025C | 0.9 | Protein kinase of unknown function |
| YDL089W | 0.6 | Protein of unknown function |
| YDR348C | 1.8 | Protein of unknown function |
| Yen1 | 364.4 | Protein of unknown function |
| YER158C | 1.2 | Protein of unknown function |
| YGR035C | 0.5 | Protein of unknown function |
| YHL035C | 1.2 | Protein of unknown function |
| YHR149C | 1.0 | Protein of unknown function |
| YJL084C | 1.3 | Protein of unknown function |
| YJR054W | 4.8 | Protein of unknown function |
| YKR078W | 0.3 | Protein of unknown function |
| YLR187W | 1.5 | Protein of unknown function |
| YLR278C | 0.9 | Protein of unknown function |
| YML119W | 0.5 | Protein of unknown function |
| YNL058C | 1.2 | Protein of unknown function |
| YNL321W | 3.1 | Member of the calcium permease family o...
| YNR047W | 4.3 | Protein kinase of unknown function |
| YOL036W | 2.6 | Protein of unknown function |
| YOL070C | 0.6 | Protein of unknown function |
| YOR066W | 1.9 | Protein of unknown function |
| YOR315W | 0.5 | Protein of unknown function |
| YPL267W | 1.6 | Protein of unknown function |
| Yrf1-3 | 1.4 | Protein of unknown function |
| Yrf1-6 | 0.7 | Protein of unknown function |
| Yta7 | 1.4 | Protein of unknown function |
| Zip1 | 3.4 | Structural protein of the synaptonemal com...
[[FrontPage]]
RIGHT:&lastmod();
ページ名:
