Table 3

Transcript/protein abundance data used for validation of expression level predictors

name

type

N

ref

Web source

Files / accessions

medium

Saccharomyces cerevisiae

Sce-1

prot

2014

[51]

http://bioinfo.mbb.yale.edu/expression/prot-v-mrna/ webcite

1.ref-abund.xls, column G

rich

Sce-2

prot

3960

[52]

http://www.nature.com/nature/journal/v425/n6959/suppinfo/nature02046.html webcite

nature02046-s2.xls

rich (YEPD)

Sce-3

mRNA

5432

[51]

http://bioinfo.mbb.yale.edu/expression/prot-v-mrna/ webcite

1.ref-abund.xls, column B

combined data

Escherichia coli K-12 MG1655

Eco-1

prot

138

[46]

http://arep.med.harvard.edu/labgc/proteom.html webcite

tables A1, A2, A3

minimal

Eco-2

prot

[79]

47

ftp://ftp.ncbi.nlm.nih.gov/repository/ECO2DBASE/edition6/ webcite

columns AB, RIC

rich

Eco-3

prot

69

[47]

ftp://ftp.ncbi.nlm.nih.gov/repository/ECO2DBASE/edition6/ webcite

columns PHNppm, PSppm, NSppm

minimal (MOPS, glucose)

Eco-4

mRNA

2597

[53]

http://www.pnas.org/cgi/content/full/112318199/DC1 webcite

3181Table6.xls, column D

rich (LB)

Eco-5

mRNA

3685

[54]

http://asap.ahabs.wisc.edu/annotation/php/logon.php webcite

EXPSET003: PALSP01-PALSP11

minimal (MOPS, glucose)

Escherichia coli K-12 W3110

Ecj-6

mRNA

3788

[55]

http://www.genome.jp/kegg/expression/ webcite

ex298 – ex320, ex328-ex334

Bacillus subtilis

Bsu-1

mRNA

3581

[56]

http://www.genome.jp/kegg/expression/ webcite

ex745 – ex749

rich (LB)

Bsu-2

mRNA

3590

[57]

http://www.genome.jp/kegg/expression/ webcite

ex264, ex265, ex272, ex273, ex275, ex276, ex278 – ex286

rich (LB)

Bsu-3

mRNA

3577

[58]

http://www.genome.jp/kegg/expression/ webcite

ex940 – ex945

DSM

Synechocystis sp. PCC6803

Syn-1

mRNA

2840

[59]

http://www.genome.jp/kegg/expression/ webcite

ex832 – ex839

low light conditions

Syn-2

mRNA

2840

[60]

http://www.genome.jp/kegg/expression/ webcite

ex22, 23, 24, 44

Plasmodium falciparum 3D7

Pfa-1

prot

1068

[61]

http://www.nature.com/nature/journal/v419/n6906/suppinfo/nature01107.html webcite

nature01107-s1.xls

average of 4 life stages

Pfa-2

mRNA

2081

[62]

http://carrier.gnf.org/publications/CellCycle/ webcite

Table_1, columns I, K, Q, AB, AD, AJ, AO, AQ

average of 4 life stages

Supek and Vlahoviček BMC Bioinformatics 2005 6:182   doi:10.1186/1471-2105-6-182