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	Network Comparison Type	green	Interaction Map	red	network_comparison

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Showing element 51 to 100 of 38536 in total

Filtered  : 1
Network Comparison Type  : Divided

description	Rank	Value Type	green	Interaction Map	red	network_comparison
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592]	3423	Ranked	196.707	Low confidence	199.702	1.01523
	3667	Squared	44025.2		45400.4	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]	2882	Measured	8175.27		7948.01	1.02859
	2991	Squared	44050.1		45624.8	1.03575
	3126	Measured	0.00001	High confidence	0.00001	1
		Ranked
		Squared
		Rooted
	3189		73.847	Low confidence	71.5946	1.03146
	3585	Ranked	199.628		202.517	1.01447
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	588	Squared	27879.3	High confidence	23526.4	1.18502
	1136	Measured	6303.92		5790.65	1.08864
	1907	Rooted	65.2789		63.4353	1.02906
	1963	Ranked	213.703		211.633	1.00978
	2182	Measured	8386.58	Low confidence	8130.62	1.03148
	2477	Rooted	75.1674		72.718	1.03368
	2659	Ranked	196.574		200.053	1.0177
	3878	Squared	44870.2		46195.2	1.02953
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891]	1632	Rooted	74.1551		71.5773	1.03601
	1693	Measured	8246.34		7981.12	1.03323
	1873	Ranked	199.455		203.414	1.01985
	2922	Measured	0.00001	High confidence	0.00001	1
		Ranked
		Squared
		Rooted
	4003	Squared	44461.5	Low confidence	45711.3	1.02811
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704]	1727		42157.3		43932.5	1.04211
	4071	Measured	8067.47		7896.47	1.02166
	4138	Rooted	73.4871		71.6344	1.02586
	4255	Ranked	200.395		202.306	1.00954
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946]	575	Measured	8965.49		8572.9	1.04579
	1143	Squared	32561.8	High confidence	28551.5	1.14046
	1272	Rooted	77.1756	Low confidence	74.3919	1.03742
	1411	Measured	6262.07	High confidence	5812.02	1.07743
	1943	Rooted	63.0838		61.3337	1.02853
	2076	Ranked	194.83	Low confidence	198.587	1.01928
	2439		221.425	High confidence	220.681	1.00337
	4439	Squared	50977.2	Low confidence	49879	1.02202
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]	1532		44795.5		46733.3	1.04326
	2834	Rooted	75.0319		72.6559	1.0327
	2864	Ranked	197.043		200.418	1.01713
	3088	Measured	0.00001	High confidence	0.00001	1
		Ranked
		Squared
		Rooted
	3095	Measured	8370.12	Low confidence	8144.39	1.02772
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312]	591		8956.98		8566.17	1.04562
	1135	Squared	32641.7	High confidence	28600.9	1.14128
	1291	Rooted	77.1362	Low confidence	74.3579	1.03736
	1415	Measured	6265.44	High confidence	5815.33	1.0774

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.