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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Filtered	Gene	Value Type	Network Comparison Type	Interaction Map	network_comparison	Rank	description	green	red

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Showing element 501 to 550 of 77072 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

Interaction Map	network_comparison	Rank	description	green	red
High confidence	17400000	2	cab2. [refseq;acc:nm_033419]	174	0.00001
	36400000	1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364
Low confidence	1	837	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]		0.00001
		838	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]
		839	cobw-like protein. [refseq;acc:nm_018491]
		840	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
		841	gamma-glutamyltransferase. [sptrembl;acc:q14390]
		842	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
		843	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
	1.00005	836	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	1589.95	1589.87
	1.0001	835	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	1573.69	1573.54
	1.00015	834	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	2710.41	2710.81
	1.0002	833	ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686]	9357.07	9355.21
	1.00033	832	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	3507.42	3506.27
	1.00065	831	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]	1242.41	1243.22
	1.00074	830	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]	3462.18	3464.75
	1.00086	829	alpha-nac protein. [sptrembl;acc:q9h009]	1465.37	1464.11
	1.00124	828	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	1464.85	1463.03
	1.0013	827	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	1673.2	1675.38
	1.00138	826	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	14901.7	14922.2
	1.00153	825	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	1594.85	1597.29
	1.00157	824	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	1595.05	1597.55
	1.00159	822	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	5046.33	5038.33
		823	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	1595.12	1597.66
	1.00161	821	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	770.408	771.651
	1.00182	820	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	1595.89	1598.8
	1.00194	819	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	4459.15	4467.8
	1.00234	818	actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996]	2071.52	2076.36
	1.00239	817	timeless homolog. [refseq;acc:nm_003920]	1148.47	1151.21
	1.00256	816	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	1264.88	1268.12
	1.00257	815	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]	3822.12	3831.93
	1.00267	814	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	6282.88	6266.18
	1.00276	813	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	9860.07	9832.89
	1.00289	812	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	1554.65	1550.17
	1.00296	811	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	6352.81	6334.04
	1.00304	810	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	969.022	966.085
	1.00317	809	dna topoisomerase i (ec 5.99.1.2). [swissprot;acc:p11387]	1763.71	1769.3
	1.00326	808	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	7115.3	7138.53
	1.00339	807	chorein (chorea-acanthocytosis protein). [swissprot;acc:q96rl7]	1505.34	1510.44
	1.00362	806	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	6099.89	6121.96
	1.00367	805	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	6193.94	6216.67
	1.00368	804	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	6179.55	6202.32
	1.00387	803	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	6330.06	6354.56
	1.00398	802	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	6779.39	6806.37
	1.00424	801	butyrate-induced transcript 1. [refseq;acc:nm_016395]	4703	4683.13
	1.00442	800	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	1259.69	1254.15
	1.00475	799	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	1475.19	1482.2
	1.00479	798	scratch; scratch 1. [refseq;acc:nm_031309]	1015.49	1020.35
	1.00489	797	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	1597.32	1605.13
	1.0051	796	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	1775.53	1784.58

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.