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

Results: HTML CSV LaTeX

Showing element 1980 to 2029 of 3228 in total

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

Rank	description	red	green	network_comparison
1980	tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5]	209.539	207.529	1.00969
1981	d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
1982	40s ribosomal protein s28. [swissprot;acc:p25112]	200.343	198.427	1.00966
1983	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	219.25	217.175	1.00955
1984	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	219.26	217.193	1.00952
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]	225.022	222.9
1988	9 kda protein. [swissprot;acc:p13994]	219.26	217.193
1989	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	219.261	217.195	1.00951
1990	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	219.26	217.194
1991	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
1992	zasp protein (fragment). [sptrembl;acc:q9y4z3]	219.267	217.207	1.00948
1993	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	189.052	190.835	1.00943
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]	189.011	190.787	1.0094
1995	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	188.961	190.73	1.00936
1996	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	204.682	202.784
1997	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	204.651	202.759	1.00933
1998	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	200.219	198.37	1.00932
1999	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	204.636	202.748	1.00931
2000	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	204.626	202.739
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]	225.02	222.948	1.00929
2002	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	214.775	216.769	1.00928
2003	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	208.315	206.41	1.00923
2004	receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303]	225.019	222.969	1.00919
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]	216.201	214.245	1.00913
2010	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]	193.517	191.766
2011	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]
2012	dead-box protein. [refseq;acc:nm_018665]
2013	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]	217.662	215.693
2014	protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480]	217.676	215.709	1.00912
2015	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	217.941	215.979	1.00908
2016	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]	199.092	197.301
2017	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	127.397	128.553	1.00907
2018	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]
2019	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]	215.799	213.865	1.00904
2020	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	223.168	221.176	1.00901
2021	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]	208.601	210.464	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	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	215.553	213.663	1.00885
2025	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	189.987	191.668
2026	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]	215.553	213.663
2027	lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362]	225.015	223.041
2028	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	215.553	213.663
2029	cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059]	189.999	191.677	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.