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 51 to 100 of 66312 in total

Filtered  : 1

description	Rank	Value Type	Interaction Map	green	red	Network Comparison Type	network_comparison
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]	280	Squared	High confidence	38866.5	30566.4	Subtracted	8300.1
	311					Divided	1.27154
	319	Measured		8532.02	7477	Subtracted	1055.02
	331	Rooted	Low confidence	79.5804	75.8843		3.6961
	378					Divided	1.04871
	514	Measured	High confidence	8532.02	7477		1.1411
	588	Ranked	Low confidence	185.859	191.507		1.03039
	631	Rooted	High confidence	78.5795	73.8577	Subtracted	4.7218
	664	Ranked	Low confidence	185.859	191.507		5.648
	822	Rooted	High confidence	78.5795	73.8577	Divided	1.06393
	1048	Ranked		182.308	187.96		1.031
	1128					Subtracted	5.652
	3936	Squared	Low confidence	47372.8	46138.2		1234.6
	4138					Divided	1.02676
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]	230	Measured		9018.94	8492.92	Subtracted	526.02
	252					Divided	1.06194
	279	Squared	High confidence	38919.9	30596.2	Subtracted	8323.7
	308					Divided	1.27205
	318	Measured		8543.66	7485.08	Subtracted	1058.58
	369	Rooted	Low confidence	79.1997	75.6219		3.5778
	427					Divided	1.04731
	513	Measured	High confidence	8543.66	7485.08		1.14143
	616	Rooted		78.6514	73.9102	Subtracted	4.7412
	637	Ranked	Low confidence	186.751	192.166	Divided	1.029
	737					Subtracted	5.415
	811	Rooted	High confidence	78.6514	73.9102	Divided	1.06415
	1043	Ranked		182.137	187.834		1.03128
	1121					Subtracted	5.697
	4331	Squared	Low confidence	47088.3	46049.4		1038.9
	4418					Divided	1.02256
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	1941	Measured		8323.04	8065.05	Subtracted	257.99
	2035					Divided	1.03199
	2688	Rooted		74.9741	72.5914	Subtracted	2.3827
	2766					Divided	1.03282
	3423	Ranked		196.707	199.702		1.01523
	3432					Subtracted	2.995
	3567	Squared		44025.2	45400.4		1375.2
	3667					Divided	1.03124
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]	2819			44050.1	45624.8	Subtracted	1574.7
	2882	Measured		8175.27	7948.01	Divided	1.02859
	2902					Subtracted	227.26
	2991	Squared		44050.1	45624.8	Divided	1.03575
	3126	Measured	High confidence	0	0	Subtracted	0
				0.00001	0.00001	Divided	1
		Ranked		0	0	Subtracted	0
				0.00001	0.00001	Divided	1
		Squared		0	0	Subtracted	0
				0.00001	0.00001	Divided	1
		Rooted		0	0	Subtracted	0
				0.00001	0.00001	Divided	1

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.