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

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Showing element 3180 to 3229 of 38536 in total

Filtered  : 0
Network Comparison Type  : Divided

description	Rank	network_comparison	green	Interaction Map	Value Type	red
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	180	1.21389	19621.3	Low confidence	Measured	23818.1
	189	1.45125	160184	High confidence	Squared	232467
	193	1.13768	111.067	Low confidence	Rooted	126.359
		1.21389	19621.3	High confidence	Measured	23818.1
	213	1.13768	111.067		Rooted	126.359
nuclear lim interactor-interacting factor 1 (nli-interacting factor 1) (nif-like protein) (ya22 protein) (hya22). [swissprot;acc:o15194]	191	1.36578	480.337	Low confidence	Squared	656.037
	376	1.09168	18.5623		Rooted	17.0034
	435	1.07486	11938.2		Ranked	12831.9
	607	1.0351	718.102		Measured	693.753
nuclear lim interactor-interacting factor 2 (nli-interacting factor 2) (protein os-4). [swissprot;acc:o14595]	190	1.36579	483.747		Squared	660.695
	380	1.08993	18.664		Rooted	17.1241
	446	1.07363	11891		Ranked	12766.5
	610	1.03491	723.073		Measured	698.679
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	2	561325	0.00001	High confidence	Squared	5.61325
		1240970			Rooted	12.4097
	8	1.89918	21888		Ranked	11525
	95	15400000	0.00001		Measured	154
	285	1.19319	3698.75	Low confidence	Squared	4413.3
	664	1.02444	1330.95		Measured	1363.48
	720	1.0168	22.9582		Rooted	23.3438
	819	1.002	11256.8		Ranked	11234.3
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	79	1.27901	12106.5	High confidence		9465.55
	219	1.13456	27.9904		Rooted	31.7569
	310	1.11276	11164.2	Low confidence	Ranked	10032.9
	391	1.08482	9878.65	High confidence	Squared	9106.26
	415	1.07835	27.2079	Low confidence	Rooted	29.3397
	458	1.01327	2668.56	High confidence	Measured	2633.61
	640	1.02757	1921.25	Low confidence		1974.21
	823	1.00289	6622.06		Squared	6603
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	47	1.31395	5700.79		Ranked	4338.65
	71			High confidence
	97	2.23326	23426.5		Squared	10489.8
				Low confidence
	103	1.46874	7500.75		Measured	5106.93
	104			High confidence
	172	1.15183	70.9983	Low confidence	Rooted	61.6393
	175			High confidence
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	33	1.52929	8691.76		Ranked	13292.2
	73	1.36418	29.828		Rooted	21.8651
	188	1.22221	1397.66		Measured	1143.55
	319	1.15612	6643.86	Low confidence	Squared	7681.13
	376	1.11487	952.74	High confidence		1062.18
	470	1.07112	1596.65	Low confidence	Measured	1710.21
	502	1.0542	23.7041		Rooted	24.9889
	604	1.03567	11587.2		Ranked	11188.1
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	63	1.34428	11453	High confidence		8519.83
	66	1.40854	21.9983		Rooted	30.9855
	73	2.9342	509.542		Squared	1495.1
	74	1.252	7386.89	Low confidence	Ranked	5900.08
	75	1.71412	925.298	High confidence	Measured	1586.07

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.