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 5258 to 5307 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
329	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Squared	Subtracted	1	19321	12542.6	6778.4
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Ranked	Divided		312	284	1.09859
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Measured			15999.1	19007.1	1.18801
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Rooted	Subtracted		124.41	117.043	7.367
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	Ranked	Divided	0	15977.3	15115.5	1.05701
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Rooted			15.4404	16.3116	1.05642
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]		Subtracted		44.9117	43.5558	1.3559
330	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Measured	Divided		1658.23	1805.52	1.08882
	60s ribosomal protein l32. [swissprot;acc:p02433]	Rooted		1	50.519	45.5497	1.1091
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Squared	Subtracted	0	220.878	173.801	47.077
	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Ranked	Divided	1	312	284	1.09859
	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]		Subtracted		224.657	203.235	21.422
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	Divided	0	57.5016	60.7262	1.05608
	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]	Measured	Subtracted	1	11773	10733.2	1039.8
	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	Ranked		0	11948.4	11295.6	652.8
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Squared	Divided		2758.07	3161.7	1.14635
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Measured	Subtracted		166.114	100.887	65.227
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Rooted			39.0883	37.7357	1.3526
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Squared	Divided	1	16203.4	20339.9	1.25529
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]		Subtracted		19321	12542.6	6778.4
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Ranked	Divided	0	12320.2	13018.5	1.05668
	septin 6. [swissprot;acc:q14141]	Measured		1	15959.9	18957.1	1.1878
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	Rooted	Subtracted		55.5965	62.9349	7.3384
331	40s ribosomal protein s3a. [swissprot;acc:p49241]	Ranked	Divided	0	10405.1	10992.4	1.05644
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Squared			26.2121	22.8932	1.14497
	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	Ranked	Subtracted		11634.4	10989.9	644.5
	alpha-nac protein. [sptrembl;acc:q9h009]	Rooted	Divided		9.95878	9.44328	1.05459
	apical-like protein (apxl protein). [swissprot;acc:q13796]			1	60.6697	67.2802	1.10896
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Measured	Subtracted	0	403.827	339.154	64.673
	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Ranked	Divided	1	312	284	1.09859
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Measured	Subtracted		10246.1	11285.8	1039.7
	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107]		Divided	0	4088	4451	1.0888
	lamin b2. [swissprot;acc:q03252]	Squared	Subtracted		539.519	494.357	45.162
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Rooted			19.4501	18.1126	1.3375
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Squared		1	19321	12542.6	6778.4
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	Rooted			55.5965	62.9349	7.3384
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Measured	Divided		20287.2	17083.8	1.18751
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Squared			33100.3	41520.6	1.25439
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Ranked	Subtracted		224.647	203.242	21.405
332	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Measured	Divided	0	15411.3	14167	1.08783
	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Rooted			15.297	14.5086	1.05434
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Measured	Subtracted		545.902	610.424	64.522
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Rooted			30.3712	31.6971	1.3259
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Squared		1	19321	12542.6	6778.4
	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	Ranked			224.633	203.251	21.382
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]			0	11634.4	10989.9	644.5
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Squared	Divided		3693.52	3232.47	1.14263
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Rooted	Subtracted	1	59.0951	66.4332	7.3381
	my016 protein. [sptrembl;acc:q9h3k6]	Squared		0	1279.28	1234.42	44.86
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Ranked	Divided		8125.5	7697.5	1.0556

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.