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

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Showing element 19220 to 19269 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	Network Comparison Type	description	network_comparison	red	green
2403	Ranked	Subtracted	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	0.784	218.2	218.984
	Squared	Divided	dymeclin. [refseq;acc:nm_017653]	1.06637	26996.7	28788.6
		Subtracted	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	1321.2	15953.2	17274.4
	Rooted	Divided	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]	1.01535	60.8344	61.7685
		Subtracted	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]	0.9375	58.6893	57.7518
2404	Measured	Divided		1.03884	5078.5	5275.76
		Subtracted	60s ribosomal protein l3-like. [swissprot;acc:q92901]	187.5	3617.81	3430.31
	Ranked	Divided	acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424]	1.0037	193.389	194.105
		Subtracted	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]	0.784	218.2	218.984
	Squared	Divided	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]	1.06637	26996.7	28788.6
		Subtracted	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	1320.8	13245.8	14566.6
	Rooted	Divided	transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8]	1.015	57.6124	58.4763
		Subtracted	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	0.9375	58.6893	57.7518
2405	Measured	Divided		1.03884	5078.5	5275.76
		Subtracted	hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3]	185.12	4457.6	4642.72
	Ranked	Divided	thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472]	1.00366	221.677	222.489
		Subtracted	upf0183 protein. [swissprot;acc:q9bsu1]	0.784	218.2	218.984
	Squared	Divided	lats homolog 1. [refseq;acc:nm_004690]	1.06637	26996.7	28788.6
		Subtracted	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	1320.6	15945.8	17266.4
	Rooted	Divided	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	1.01491	60.6732	61.5778
		Subtracted	bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]	0.9375	58.6893	57.7518
2406	Measured	Divided		1.03884	5078.5	5275.76
		Subtracted	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	184.6	3544.03	3359.43
	Ranked	Divided	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	1.00366	182.563	183.232
		Subtracted	antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]	0.784	218.2	218.984
	Squared	Divided	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	1.06637	26996.7	28788.6
		Subtracted	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	1320.3	13244.1	14564.4
	Rooted	Divided	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	1.01487	58.7808	57.9198
		Subtracted	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]	0.9375	58.6893	57.7518
2407	Measured	Divided		1.03884	5078.5	5275.76
		Subtracted	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	184.6	3544.03	3359.43
	Ranked	Divided	proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720]	1.00364	214.234	213.456
		Subtracted	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232]	0.784	218.2	218.984
	Squared	Divided	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]	1.06637	26996.7	28788.6
		Subtracted	40s ribosomal protein s16. [swissprot;acc:p17008]	1320.3	13244.1	14564.4
	Rooted	Divided	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]	1.01487	58.7808	57.9198
		Subtracted	serpin b11. [swissprot;acc:q96p15]	0.9375	58.6893	57.7518
2408	Measured	Divided		1.03884	5078.5	5275.76
		Subtracted	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	183.26	5454.62	5637.88
	Ranked	Divided	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	1.00362	194.407	193.706
		Subtracted	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]	0.784	218.2	218.984
	Squared	Divided	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]	1.06637	26996.7	28788.6
		Subtracted	rad50-interacting protein 1. [refseq;acc:nm_021930]	1309.03	48.0356	1357.07
	Rooted	Divided	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172]	1.01487	58.7808	57.9198
		Subtracted	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	0.9375	58.6893	57.7518
2409	Measured	Divided		1.03884	5078.5	5275.76
		Subtracted	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	182.75	4857.03	5039.78
	Ranked	Divided	lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760]	1.00362	194.407	193.706
		Subtracted	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133]	0.784	218.2	218.984
	Squared	Divided	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]	1.06637	26996.7	28788.6

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.