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

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Showing element 4058 to 4107 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2029	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	Subtracted	220.8	222.61	1.81
2030	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]	Divided	189.999	191.677	1.00883
	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	Subtracted	218.79	216.981	1.809
2031	oxidation resistance 1. [refseq;acc:nm_181354]
	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	Divided	218.466	216.562	1.00879
2032	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]		215.322	213.46	1.00872
	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	Subtracted	223.199	225.008	1.809
2033	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]	Divided	215.322	213.46	1.00872
	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]	Subtracted	218.79	216.981	1.809
2034	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	Divided	218.919	220.812	1.00865
	dymeclin. [refseq;acc:nm_017653]	Subtracted	218.79	216.981	1.809
2035	centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]	Divided	218.919	220.812	1.00865
	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]	Subtracted	218.79	216.981	1.809
2036	lamin b1. [swissprot;acc:p20700]	Divided	218.919	220.813	1.00865
	lats homolog 1. [refseq;acc:nm_004690]	Subtracted	218.79	216.981	1.809
2037	centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]	Divided	218.919	220.812	1.00865
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	Subtracted	218.79	216.981	1.809
2038	lamin a/c (70 kda lamin). [swissprot;acc:p02545]	Divided	218.92	220.811	1.00864
	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]	Subtracted	218.79	216.981	1.809
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]	Divided	190.551	192.191	1.00861
	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]	Subtracted	218.79	216.981	1.809
2040	brachyury protein (t protein). [swissprot;acc:o15178]	Divided	210.586	208.803	1.00854
	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]	Subtracted	218.79	216.981	1.809
2041	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]	Divided	196.808	195.141	1.00854
	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]	Subtracted	218.79	216.981	1.809
2042	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	1.791
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Divided	210.586	208.803	1.00854
2043	brachyury protein (t protein). [swissprot;acc:o15178]	Subtracted			1.783
	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	Divided	196.837	195.173	1.00853
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	198.24	1.00851
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Subtracted	210.586	208.803	1.783
2045	huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]		189.052	190.835
	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	Divided	199.928	198.24	1.00851
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]
	cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	Subtracted	221.703	223.483	1.78
2047	peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526]
	solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3]	Divided	224.124	226.003	1.00838
2048	iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413]	Subtracted	221.703	223.483	1.78
	solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]	Divided	224.124	226.003	1.00838
2049	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]	Subtracted	189.011	190.787	1.776
	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	Divided	220.787	222.634	1.00837
2050	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	Subtracted	188.961	190.73	1.769
	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	Divided	218.79	216.981	1.00834
2051	oxidation resistance 1. [refseq;acc:nm_181354]
	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	Subtracted	214.328	212.561	1.767
2052	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	Divided	207.667	205.95	1.00834
	tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814]	Subtracted	193.517	191.766	1.751
2053	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]	Divided	218.79	216.981	1.00834
	putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305]	Subtracted	193.517	191.766	1.751
2054	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.