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

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Showing element 1 to 50 of 19268 in total

Value Type  : Ranked

description	Rank	Network Comparison Type	Filtered	red	Interaction Map	network_comparison	green
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	Divided	1	185.678	High confidence	1.32082	245.247
	54	Subtracted				59.569
	172		0	15260.6		1364.8	13895.8
	242	Divided				1.09822
	600	Subtracted		13205.3	Low confidence	385	13590.3
	629	Divided				1.02915
	4130		1	199.383		1.01062	201.5
	4141	Subtracted				2.117
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	1038	Divided		186.741	High confidence	1.03148	181.041
	1120	Subtracted				5.7
	1328	Divided		198.342	Low confidence	1.02218	194.038
	1408	Subtracted				4.304
1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	1032	Divided		186.664	High confidence	1.03162	180.943
	1115	Subtracted				5.721
	1322	Divided		198.322	Low confidence	1.0222	194.014
	1406	Subtracted				4.308
1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5]	588	Divided		191.507		1.03039	185.859
	664	Subtracted				5.648
	1048	Divided		187.96	High confidence	1.031	182.308
	1128	Subtracted				5.652
1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7]	637	Divided		192.166	Low confidence	1.029	186.751
	737	Subtracted				5.415
	1043	Divided		187.834	High confidence	1.03128	182.137
	1121	Subtracted				5.697
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	3423	Divided		199.702	Low confidence	1.01523	196.707
	3432	Subtracted				2.995
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147]	3126	Divided		0.00001	High confidence	1	0.00001
		Subtracted		0		0	0
	3567			202.517	Low confidence	2.889	199.628
	3585	Divided				1.01447
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	1933	Subtracted		211.633	High confidence	2.07	213.703
	1963	Divided				1.00978
	2659			200.053	Low confidence	1.0177	196.574
	2668	Subtracted				3.479
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	1795			203.414		3.959	199.455
	1873	Divided				1.01985
	2922			0.00001	High confidence	1	0.00001
		Subtracted		0		0	0
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704]	4255	Divided		202.306	Low confidence	1.00954	200.395
	4263	Subtracted				1.911
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	2076	Divided		198.587		1.01928	194.83
	2165	Subtracted				3.757
	2421			220.681	High confidence	0.744	221.425
	2439	Divided				1.00337
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655]	2864			200.418	Low confidence	1.01713	197.043
	2895	Subtracted				3.375
	3088	Divided		0.00001	High confidence	1	0.00001
		Subtracted		0		0	0
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	2108	Divided		198.65	Low confidence	1.01923	194.902
	2185	Subtracted				3.748

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.