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 1823 to 1872 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
114	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Rooted	Divided	0	14.7363	18.7165	1.27009
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Squared			35.0828	69.7867	1.9892
115	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]	Measured	Subtracted		305.45	26.1599	279.29
	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Divided	1	21185	28492	1.34491
	40s ribosomal protein s26. [swissprot;acc:p02383]	Rooted	Subtracted	0	9.92134	5.66499	4.25635
	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Squared	Divided		105.615	53.4024	1.97772
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Rooted	Subtracted	1	21.4476	36.9459	15.4983
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Squared	Divided		19321	12542.6	1.54043
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Ranked	Subtracted	0	11124.8	13005.3	1880.5
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Rooted	Divided		18.4959	14.5738	1.26912
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Ranked	Subtracted	1	277.546	240.461	37.085
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]		Divided		332.874	267.246	1.24557
	pnas-18. [sptrembl;acc:q9bzu3]	Measured	Subtracted		13680.5	11409.6	2270.9
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Squared		0	6027.87	7086.08	1058.21
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]			1	72886.3	98544.5	25658.2
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Rooted	Divided		80.4705	101.526	1.26165
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Ranked		0	18662.8	15627	1.19427
	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	Measured			385	543	1.41039
116	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]				668	475	1.40632
	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Rooted		1	80.4705	101.526	1.26165
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Measured	Subtracted	0	1382.5	1107	275.5
	dead-box protein. [refseq;acc:nm_018665]	Squared	Divided		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

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.