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	network_comparison	green

Results: HTML CSV LaTeX

Showing element 2001 to 2050 of 3228 in total

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

Rank	description	red	network_comparison	green
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	1.00929	222.948
2002	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	214.775	1.00928	216.769
2003	axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	208.315	1.00923	206.41
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	1.00919	222.969
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	1.00913	214.245
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	1.00912	215.709
2015	dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472]	217.941	1.00908	215.979
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	1.00907	128.553
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	1.00904	213.865
2020	putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153]	223.168	1.00901	221.176
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	1.00893	210.464
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	1.00885	213.663
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	1.00883	191.677
2030	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]
2031	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	218.466	1.00879	216.562
2032	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	215.322	1.00872	213.46
2033	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
2034	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	218.919	1.00865	220.812
2035	centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
2036	lamin b1. [swissprot;acc:p20700]			220.813
2037	centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]			220.812
2038	lamin a/c (70 kda lamin). [swissprot;acc:p02545]	218.92	1.00864	220.811
2039	acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	190.551	1.00861	192.191
2040	brachyury protein (t protein). [swissprot;acc:o15178]	210.586	1.00854	208.803
2041	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	196.808		195.141
2042	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	210.586		208.803
2043	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	196.837	1.00853	195.173
2044	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]	199.928	1.00851	198.24
2045	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]
2046	adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
2047	solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3]	224.124	1.00838	226.003
2048	solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
2049	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	220.787	1.00837	222.634
2050	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	218.79	1.00834	216.981

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.