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

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Showing element 1 to 50 of 77072 in total

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

network_comparison	Interaction Map	Rank	red	green	description
1	High confidence	494	0.00001	0.00001	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
		495			histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
		496			mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]
		497			histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
		498			translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
		499			homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]
		500			rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]
		501			h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
		502			brca1 associated protein. [refseq;acc:nm_006768]
	Low confidence	837			gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
		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	1589.87	1589.95	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]
1.0001		835	1573.54	1573.69	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]
1.00015		834	2710.81	2710.41	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]
1.0002		833	9355.21	9357.07	ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686]
1.00033		832	3506.27	3507.42	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]
1.00059	High confidence	493	2410.35	2411.78	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.00065	Low confidence	831	1243.22	1242.41	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]
1.00074		830	3464.75	3462.18	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803]
1.00086		829	1464.11	1465.37	alpha-nac protein. [sptrembl;acc:q9h009]
1.00124		828	1463.03	1464.85	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]
1.0013		827	1675.38	1673.2	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]
1.00138		826	14922.2	14901.7	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]
1.00153		825	1597.29	1594.85	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]
1.00157		824	1597.55	1595.05	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
1.00159	High confidence	492	5038.33	5046.33	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]
	Low confidence	822
		823	1597.66	1595.12	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
1.00161		821	771.651	770.408	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]
1.00182		820	1598.8	1595.89	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
1.00194		819	4467.8	4459.15	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]
1.00223	High confidence	491	22962	22910.9	high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]
1.00224		489	22946.3	22895.1	dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]
		490	22940.1	22888.8	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]
1.00225		487	250.419	249.857	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]
		488			ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1.00227		486	22878.7	22826.8	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]
1.00229		485	22850.1	22797.8	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]
1.00234	Low confidence	818	2076.36	2071.52	actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996]
1.00239		817	1151.21	1148.47	timeless homolog. [refseq;acc:nm_003920]
1.00256		816	1268.12	1264.88	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]
1.00257		815	3831.93	3822.12	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]
1.00267		814	6266.18	6282.88	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]
1.00276		813	9832.89	9860.07	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]
1.00278	High confidence	484	958.429	961.098	scribble. [refseq;acc:nm_015356]

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.