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 1844 to 1893 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
116	dead-box protein. [refseq;acc:nm_018665]	Squared	Divided	0	37.7545	19.3759	1.94853
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Ranked	Subtracted		11123.4	13000.1	1876.7
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Rooted	Divided		9.7842	7.75282	1.26202
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]		Subtracted	1	40.6302	25.4452	15.185
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Ranked	Divided		268.565	334.483	1.24545
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]		Subtracted		208.52	171.595	36.925
	metaxin 1. [swissprot;acc:q13505]		Divided	0	13761.3	16422.1	1.19335
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Squared		1	19321	12542.6	1.54043
	p66 alpha. [refseq;acc:nm_017660]		Subtracted		81888.8	56306.5	25582.3
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Measured	Divided		21185	28492	1.34491
	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]	Rooted	Subtracted	0	0	4.24264	4.24264
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	Measured		1	13261.9	11017.8	2244.1
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Squared		0	7372.32	6325.27	1047.05
117	60s ribosomal protein l9. [swissprot;acc:p32969]				4941.26	5985.86	1044.6
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Ranked	Divided		11545	13771.5	1.19285
	block 23. [sptrembl;acc:q8nhw5]		Subtracted		11469.3	13334.8	1865.5
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Measured			1161.88	891.114	270.766
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Squared	Divided	1	211446	137422	1.53866
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Rooted	Subtracted		40.5691	25.4263	15.1428
	high-mobility group 20a. [refseq;acc:nm_018200]	Ranked			208.588	171.778	36.81
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Measured			9276.47	7090.37	2186.1
	neuralized-like. [refseq;acc:nm_004210]	Ranked	Divided		332.326	266.948	1.24491
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured			21185	28492	1.34491
	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Rooted		0	26.63	33.5888	1.26131
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]		Subtracted		4.24264	0	4.24264
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Squared	Divided		0.545459	1.05706	1.93793
	transcription factor jun-b. [swissprot;acc:p17275]	Rooted		1	63.4173	79.5311	1.25409
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Squared	Subtracted		81888.8	56306.5	25582.3
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	Divided	0	170.5	122	1.39754
118	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Squared	Subtracted		4121.56	5159.2	1037.64
	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Ranked	Divided		12049	14370.7	1.19269
	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Measured	Subtracted	1	9275.1	7089.65	2185.45
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Ranked		0	3845	5699	1854
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Measured			324.442	593.094	268.652
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Rooted	Divided	1	50.3065	62.9788	1.2519
	methyltransferase like 2. [refseq;acc:nm_018396]	Measured		0	31	43	1.3871
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Rooted			9.1258	11.4849	1.25851
	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09]	Ranked		1	284.753	228.934	1.24382
		Rooted	Subtracted		37.2205	52.2064	14.9859
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Ranked			274.027	237.79	36.237
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Measured	Divided		21185	28492	1.34491
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Squared			210445	136779	1.53858
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]			0	240.689	124.83	1.92813
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Rooted	Subtracted		32.6268	28.4118	4.215
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared		1	81888.8	56306.5	25582.3
119	40s ribosomal protein s29. [swissprot;acc:p30054]			0	5295.67	6326.82	1031.15
	60s ribosomal protein l7. [swissprot;acc:p18124]	Rooted			27.512	31.7228	4.2108
	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	Measured		1	12998.5	15138.2	2139.7
	adiponectin receptor 2. [refseq;acc:nm_024551]	Ranked			281.582	246.371	35.211
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared			81606.8	56215.8	25391

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.