MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Gene	Value Type	Network Comparison Type	Rank	description	Interaction Map	network_comparison	green	red	Filtered

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Showing element 1963 to 2012 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	network_comparison	green	red
1963	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	1.00978	213.703	211.633
1964	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]
1965	alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611]		222.258	224.432
1966	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8]		213.703	211.633
1967	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]		213.702	211.632
1968	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303]		213.703	211.633
1969	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
1970	importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131]	1.00975	213.683	211.62
1971	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]	1.00974	196.346	198.258
1972	regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	1.00973	217.659	219.777
1973	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]	1.00972	212.546	214.611
1974	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]
1975	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]
1976	rest corepressor. [refseq;acc:nm_015156]
1977	homolog of yeast maf1. [refseq;acc:nm_032272]	1.00969	207.529	209.539
1978	tumor differentially expressed protein 2. [refseq;acc:nm_178865]
1979	tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530]
1980	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]
1981	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1982	40s ribosomal protein s28. [swissprot;acc:p25112]	1.00966	198.427	200.343
1983	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	1.00955	217.175	219.25
1984	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	1.00952	217.193	219.26
1985	mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]
1986	65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
1987	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]		222.9	225.022
1988	9 kda protein. [swissprot;acc:p13994]		217.193	219.26
1989	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	1.00951	217.195	219.261
1990	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]		217.194	219.26
1991	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
1992	zasp protein (fragment). [sptrembl;acc:q9y4z3]	1.00948	217.207	219.267
1993	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	1.00943	190.835	189.052
1994	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	1.0094	190.787	189.011
1995	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	1.00936	190.73	188.961
1996	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]		202.784	204.682
1997	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	1.00933	202.759	204.651
1998	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	1.00932	198.37	200.219
1999	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	1.00931	202.748	204.636
2000	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]		202.739	204.626
2001	lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165]	1.00929	222.948	225.02
2002	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	1.00928	216.769	214.775
2003	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	1.00923	206.41	208.315
2004	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303]	1.00919	222.969	225.019
2005	epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]		222.971
2006	receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626]
2007	2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]		222.969
2008	receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860]
2009	proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306]	1.00913	214.245	216.201
2010	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]		191.766	193.517
2011	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
2012	dead-box protein. [refseq;acc:nm_018665]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.