BNA: Biological Network Analysis : Yeast Genomics Resources

October 02, 2012, at 09:56 AM by 12.13.176.132 -

Added lines 35-38:

http://www.yeastnet.org/ , predicted network
pixie at Princeton, predicted network

May 19, 2012, at 12:23 PM by 12.13.176.132 -

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to:

Sherlock lab
Siegal lab
Fay lab

May 17, 2012, at 10:47 AM by 12.13.176.132 -

Added lines 79-81:

Chemogenomics

http://chemogenomics.stanford.edu:16080/supplements/global/download.html

March 31, 2012, at 04:02 PM by 76.123.118.17 -

Changed lines 31-32 from:

genetic interaction:

to:

genetic interactions:
By double-deletion assay, Costanzo 2010 Science

March 27, 2012, at 04:02 PM by 12.35.54.5 -

Changed lines 65-71 from:

Stanford fitness measures.

to:

Yeast deletion project, fitness data

http://www-deletion.stanford.edu/YDPM/YDPM_index.html

Yeast fitness database

http://fitdb.stanford.edu/

Changed line 74 from:

Yeast morphology database

to:

Yeast morphology database (SCMD)

March 23, 2012, at 10:28 PM by 12.13.176.132 -

Changed lines 15-16 from:

to:

http://genome.wustl.edu/genomes/saccharomyces_cerevisiae_strain_project_genomes

February 06, 2012, at 12:45 PM by 12.13.176.132 -

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[[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS\\

to:

MPact @ MIPS and FTP site

February 06, 2012, at 12:44 PM by 12.13.176.132 -

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For protein interaction data, see:\\

to:

Interaction data,

February 06, 2012, at 12:43 PM by 12.13.176.132 -

Changed lines 25-29 from:

For protein interaction data, see:
DIP http://dip.doe-mbi.ucla.edu/ (Registration is required. Pairwise data is provided)
[[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS

BIND

to:

For protein interaction data, see:\\

DIP http://dip.doe-mbi.ucla.edu/ (Registration is required. Pairwise data is provided)
* [[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS
* BIND

February 06, 2012, at 12:42 PM by 12.13.176.132 -

Changed line 27 from:

MIPS \\

to:

[[http://mips.helmholtz-muenchen.de/genre/proj/mpact/ | MPact @ MIPS

February 06, 2012, at 10:53 AM by 12.13.176.132 -

Changed lines 3-4 from:

Strains
* Deletion collection, Open Biosystem

to:

Strains
Deletion collection, Open Biosystem, now at Invitrogen

February 06, 2012, at 10:52 AM by 12.13.176.132 -

Changed lines 4-5 from:

 Deletion collection, Open Biosystem

Deletion collection at Invitrogen

to:

Deletion collection, Open Biosystem
Deletion collection, GFP colleciton at Invitrogen

February 06, 2012, at 10:37 AM by 12.13.176.132 -

Changed line 114 from:

Labs to follow\\

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Labs to follow

February 06, 2012, at 10:37 AM by 12.13.176.132 -

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Reviews

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Reviews\\

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Labs to follow

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Labs to follow\\

February 06, 2012, at 10:36 AM by 12.13.176.132 -

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Positive selection for elevated gene expression noise in yeast

Labs to follow

to:

Positive selection for elevated gene expression noise in yeast, George Zhang's lab

Reviews [[http://www.ncbi.nlm.nih.gov/pubmed/19743424 | Proteomics. 2009 Oct;9(20):4731-43. Recent advances in yeast organelle and membrane proteomics. Premsler T, Zahedi RP, Lewandrowski U, Sickmann A.]]

Labs to follow

February 06, 2012, at 10:32 AM by 12.13.176.132 -

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protein localization

Nature. 2003 Oct 16;425(6959):686-91. Global analysis of protein localization in budding yeast. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK.

February 06, 2012, at 10:29 AM by 12.13.176.132 -

Changed line 107 from:

Boone lab

to:

Boone lab

February 06, 2012, at 10:27 AM by 12.13.176.132 -

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Boone lab

February 06, 2012, at 10:26 AM by 12.13.176.132 -

Changed line 106 from:

to:

Labs to follow

February 06, 2012, at 10:26 AM by 12.13.176.132 -

Changed lines 106-109 from:

Botstein lab Oshea lab Weismann lab

to:

Botstein lab
Oshea lab
Weismann lab

February 06, 2012, at 10:26 AM by 12.13.176.132 -

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to:

Positive selection for elevated gene expression noise in yeast

Botstein lab Oshea lab Weismann lab

February 06, 2012, at 10:15 AM by 12.13.176.132 -

Changed lines 38-41 from:

to:

protein expression noise
Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441: 840–846

February 06, 2012, at 10:03 AM by 12.13.176.132 -

Changed lines 35-41 from:

protein abundance

[[http://www.ncbi.nlm.nih.gov/pubmed/14562106 | S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature, 2003, 425, 737–741.]]

to:

protein abundance
S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature, 2003, 425, 737–741.

February 06, 2012, at 10:02 AM by 12.13.176.132 -

Added line 36:

[[http://www.ncbi.nlm.nih.gov/pubmed/14562106 |

Changed lines 39-41 from:

2003, 425, 737–741.

to:

2003, 425, 737–741.]]

February 06, 2012, at 10:01 AM by 12.13.176.132 -

Added lines 35-40:

protein abundance

S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O’Shea and J. S. Weissman, Nature, 2003, 425, 737–741.

February 06, 2012, at 09:44 AM by 12.13.176.132 -

Added lines 90-98:

Complex data Nature 440, 637-643 (30 March 2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae http://www.nature.com/nature/journal/v440/n7084/full/nature04670.html

December 21, 2011, at 04:54 PM by 12.13.176.132 -

Added lines 85-89:

Molecular Systems Biology 4; Article number 179; doi:10.1038/msb.2008.16 The role of disorder in interaction networks: a structural analysis Philip M Kim1,5,*, Andrea Sboner1,5, Yu Xia2 and Mark Gerstein1,3,4,*

December 21, 2011, at 10:26 AM by 12.13.176.132 -

Added lines 81-84:

Molecular Biology of the Cell Vol. 16, 5410–5417, November 2005 Role of Essential Genes in Mitochondrial Morphogenesis in Saccharomyces cerevisiae□D Katrin Altmann* and Benedikt Westermann

December 19, 2011, at 06:46 PM by 12.13.176.132 -

Changed lines 76-78 from:

Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc

to:

Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc, PNAS

Comparative analysis of gene expression and regulation of replicative aging associated genes in S. cerevisiaew Sukhraj Pal Singh Dhami,a Nitish Mittal,ab Sarath Chandra Jangab and Nilanjan Roy

December 19, 2011, at 05:51 PM by 12.13.176.132 -

Changed lines 75-78 from:

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Evidence for widespread adaptive evolution of gene expression in budding yeast Hunter B. Frasera,1, Alan M. Mosesb, and Eric E. Schadtc

December 18, 2011, at 07:08 PM by 12.13.176.132 -

Added lines 68-75:

Mol Biol Cell. 2011 Apr;22(7):988-98. Epub 2011 Feb 2. The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures. Davidson GS, Joe RM, Roy S, Meirelles O, Allen CP, Wilson MR, Tapia PH, Manzanilla EE, Dodson AE, Chakraborty S, Carter M, Young S, Edwards B, Sklar L, Werner-Washburne M. http://www.ncbi.nlm.nih.gov/pubmed/21289090

December 16, 2011, at 10:39 AM by 12.13.176.132 -

Added lines 64-67:

Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis David C Hess, Chad L Myers, Curtis Huttenhower, Matthew A Hibbs, Alicia P Hayes, Jadine Paw, John J Clore, Rosa M Mendoza, Bryan San Luis, Corey Nislow, Guri Giaever, Michael Costanzo, Olga G Troyanskaya, Amy A Caudy (2009), PLoS Genetics 5 (3) p. 16

August 22, 2011, at 11:54 AM by 12.13.176.132 -

Changed lines 6-7 from:

to:

http://www.cbs.knaw.nl/

August 15, 2011, at 04:59 PM by 12.13.176.132 -

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Supplementary information From the following article Quantification of the yeast transcriptome by single-molecule sequencing Doron Lipson, Tal Raz, Alix Kieu, Daniel R Jones, Eldar Giladi, Edward Thayer, John F Thompson, Stan Letovsky, Patrice Milos & M

July 16, 2011, at 11:18 PM by 68.199.68.103 -

Added lines 13-14:

 Princeton ftp site

July 16, 2011, at 11:15 PM by 68.199.68.103 -

Added lines 57-58:

Natural variation
Joseph Schacherer

July 12, 2011, at 12:04 PM by 143.48.10.68 -

Added lines 35-37:

mRNA FISH data

 Botstein lab.

June 17, 2011, at 01:09 PM by 128.112.118.72 -

Changed line 7 from:

Positive selection markers

to:

Positive selection markers\\

June 17, 2011, at 01:09 PM by 128.112.118.72 -

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URA3 LYS2 LEU2(?)

to:

 URA3 LYS2 LEU2(?)

June 17, 2011, at 01:07 PM by 128.112.118.72 -

Changed lines 8-9 from:

URA3 LYS2 LEU2(?)

to:

URA3 LYS2 LEU2(?)

June 17, 2011, at 01:07 PM by 128.112.118.72 -

Changed lines 5-6 from:

Deletion colleciton at Invitrogen

to:

Deletion collection at Invitrogen
Positive selection markers

URA3 LYS2 LEU2(?)

June 13, 2011, at 02:18 PM by 140.180.34.151 -

Changed lines 45-50 from:

to:

Stanford fitness measures. multiple sources. Austria.

Yeast morphology database

http://yeast.gi.k.u-tokyo.ac.jp/datamine/

June 13, 2011, at 02:16 PM by 140.180.34.151 -

Deleted lines 6-7:

Deleted line 25:

Added lines 37-45:

Yeast metabolic cycle

http://www.genomics.princeton.edu/~nslavov/ymc/metabolites.html

cell cycle

http://genomics.princeton.edu/~nslavov/grr_html/transcripts.html

growth curves

June 09, 2011, at 09:41 AM by 128.112.118.21 -

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to:

Deletion colleciton at Invitrogen

June 04, 2011, at 03:15 PM by 140.180.34.122 -

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Strains

Deletion collection, Open Biosystem

to:

Strains
Deletion collection, Open Biosystem

June 04, 2011, at 03:15 PM by 140.180.34.122 -

Added lines 3-6:

Strains

Deletion collection, Open Biosystem

March 06, 2009, at 01:51 PM by 76.123.113.149 -

Added lines 31-33:

Expression and aging
CLS, Longo

March 06, 2009, at 01:11 PM by 76.123.113.149 -

Changed lines 6-7 from:

to:

Changed lines 9-10 from:

 Genolevures, Sce relatives

to:

 Genolevures, Sce relatives

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to:

March 06, 2009, at 01:09 PM by 76.123.113.149 -

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 NCBI, Sce sequences

to:

 NCBI, Sce sequences
 Sanger Sce project

March 06, 2009, at 12:55 PM by 76.123.113.149 -

Changed line 3 from:

Genomes of Sce:

to:

Genomes of Sce: \\

Changed line 9 from:

UCSC genome browser on yeast

to:

UCSC genome browser on yeast \\

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protein half lives:

to:

protein half lives:\\

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mRNA half lives:

to:

mRNA half lives:\\

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Cell cycle

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Cell cycle \\

March 06, 2009, at 12:54 PM by 76.123.113.149 -

Changed lines 3-10 from:

Genomes:

 NCBI Sce sequences

Genolevures

UCSC genome browser on yeast

to:

Genomes of Sce:

 NCBI, Sce sequences

Genomes of Sce relatives:
Genolevures, Sce relatives
UCSC genome browser on yeast

Changed line 13 from:

For protein interaction data, see:\\

to:

For protein interaction data, see:\\

Changed lines 18-21 from:

genetic interaction:

protein half lives:

to:

genetic interaction:
protein half lives:

Changed line 24 from:

mRNA half lives:

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mRNA half lives:

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Cell cycle

to:

Cell cycle

March 06, 2009, at 12:52 PM by 76.123.113.149 -

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SGD CGD

to:

Genomes:

 NCBI Sce sequences

November 28, 2008, at 07:30 PM by 76.123.119.30 -

Added lines 26-27:

Cell cycle

 expression and cell cycle

November 17, 2008, at 12:41 PM by 74.254.146.120 -

Added line 7:

November 17, 2008, at 12:41 PM by 74.254.146.120 -

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to:

UCSC genome browser on yeast

 http://hgdownload.cse.ucsc.edu/downloads.html#yeast

November 17, 2008, at 12:38 PM by 74.254.146.120 -

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SGD CGD

Genolevures

Deleted line 21:

Genolevures

November 17, 2008, at 12:37 PM by 74.254.146.120 -

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genetic interaction:

November 17, 2008, at 12:37 PM by 74.254.146.120 -

Changed lines 13-15 from:

 http://mbe.oxfordjournals.org/cgi/reprint/22/6/1403

to:

 http://mbe.oxfordjournals.org/cgi/reprint/22/6/1403

Genolevures

October 22, 2008, at 09:20 AM by 75.143.68.139 -

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  Archana Belle etal PNAS 2006

to:

  Archana Belle etal PNAS 2006

mRNA half lives:

 http://mbe.oxfordjournals.org/cgi/reprint/22/6/1403

October 20, 2008, at 04:43 PM by 192.203.127.3 -

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protein half lives:

  Archana Belle etal PNAS 2006

March 23, 2006, at 05:16 PM by 128.151.242.80 -

Changed line 4 from:

[[DIP]http://dip.doe-mbi.ucla.edu/] (Registration is required. Pairwise data is provided)\\

to:

DIP http://dip.doe-mbi.ucla.edu/ (Registration is required. Pairwise data is provided)\\

March 23, 2006, at 05:15 PM by 128.151.242.80 -

Changed lines 4-8 from:

DIP (Registration is required. Pairwise data is provided)
MIPS BIND

to:

[[DIP]http://dip.doe-mbi.ucla.edu/] (Registration is required. Pairwise data is provided)
MIPS
BIND

March 23, 2006, at 05:14 PM by 128.151.242.80 -

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The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched. \\

to:

The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched.

For protein interaction data, see:
DIP (Registration is required. Pairwise data is provided)
MIPS BIND

March 23, 2006, at 05:12 PM by 128.151.242.80 -

Added line 1:

The budding yeast Saccharomyces ceresivisiae has been a model of choice for genomic studies. So far, the yeast genome is the best annotated eukaryotic genome, its protein interaction network has the best coverage and quality, its gene profiling data is one of the largest ones, its collections of mutants is unmatched. \\

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