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

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Showing element 1980 to 2029 of 3228 in total

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

Rank	green	red	description	network_comparison
1980	207.529	209.539	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]	1.00969
1981			d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1982	198.427	200.343	40s ribosomal protein s28. [swissprot;acc:p25112]	1.00966
1983	217.175	219.25	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	1.00955
1984	217.193	219.26	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	1.00952
1985			mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]
1986			65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
1987	222.9	225.022	lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664]
1988	217.193	219.26	9 kda protein. [swissprot;acc:p13994]
1989	217.195	219.261	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	1.00951
1990	217.194	219.26	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]
1991			transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
1992	217.207	219.267	zasp protein (fragment). [sptrembl;acc:q9y4z3]	1.00948
1993	190.835	189.052	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	1.00943
1994	190.787	189.011	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
1995	190.73	188.961	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	1.00936
1996	202.784	204.682	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]
1997	202.759	204.651	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	1.00933
1998	198.37	200.219	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	1.00932
1999	202.748	204.636	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	1.00931
2000	202.739	204.626	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]
2001	222.948	225.02	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
2002	216.769	214.775	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	1.00928
2003	206.41	208.315	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	1.00923
2004	222.969	225.019	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
2005	222.971		epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533]
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	222.969		2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83]
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	214.245	216.201	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
2010	191.766	193.517	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]
2011			putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
2012			dead-box protein. [refseq;acc:nm_018665]
2013	215.693	217.662	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]
2014	215.709	217.676	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	1.00912
2015	215.979	217.941	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	1.00908
2016	197.301	199.092	electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134]
2017	128.553	127.397	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	1.00907
2018			serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
2019	213.865	215.799	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	1.00904
2020	221.176	223.168	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	1.00901
2021	210.464	208.601	hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6]	1.00893
2022			atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
2023			guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3]
2024	213.663	215.553	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	1.00885
2025	191.668	189.987	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]
2026	213.663	215.553	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]
2027	223.041	225.015	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]
2028	213.663	215.553	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]
2029	191.677	189.999	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059]	1.00883

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.