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

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Showing element 1 to 50 of 16578 in total

Value Type  : Ranked
Filtered  : 1

description	Rank	Interaction Map	green	red	Network Comparison Type	network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	18	High confidence	245.247	185.678	Divided	1.32082
	54				Subtracted	59.569
	4130	Low confidence	201.5	199.383	Divided	1.01062
	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	High confidence	181.041	186.741	Divided	1.03148
	1120				Subtracted	5.7
	1328	Low confidence	194.038	198.342	Divided	1.02218
	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	High confidence	180.943	186.664	Divided	1.03162
	1115				Subtracted	5.721
	1322	Low confidence	194.014	198.322	Divided	1.0222
	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		185.859	191.507	Divided	1.03039
	664				Subtracted	5.648
	1048	High confidence	182.308	187.96	Divided	1.031
	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	Low confidence	186.751	192.166	Divided	1.029
	737				Subtracted	5.415
	1043	High confidence	182.137	187.834	Divided	1.03128
	1121				Subtracted	5.697
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	3423	Low confidence	196.707	199.702	Divided	1.01523
	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	High confidence	0	0		0
			0.00001	0.00001	Divided	1
	3567	Low confidence	199.628	202.517	Subtracted	2.889
	3585				Divided	1.01447
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	1933	High confidence	213.703	211.633	Subtracted	2.07
	1963				Divided	1.00978
	2659	Low confidence	196.574	200.053		1.0177
	2668				Subtracted	3.479
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	1795		199.455	203.414		3.959
	1873				Divided	1.01985
	2922	High confidence	0	0	Subtracted	0
			0.00001	0.00001	Divided	1
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704]	4255	Low confidence	200.395	202.306		1.00954
	4263				Subtracted	1.911
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	2076		194.83	198.587	Divided	1.01928
	2165				Subtracted	3.757
	2421	High confidence	221.425	220.681		0.744
	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	Low confidence	197.043	200.418		1.01713
	2895				Subtracted	3.375
	3088	High confidence	0	0		0
			0.00001	0.00001	Divided	1
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	2108	Low confidence	194.902	198.65		1.01923
	2185				Subtracted	3.748
	2391	High confidence	221.51	220.683		0.827
	2396				Divided	1.00375
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758]	1035	Low confidence	196.966	201.723	Subtracted	4.757
	1044				Divided	1.02415

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.