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

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Showing element 551 to 600 of 77072 in total

Filtered  : 0
Value Type  : Measured

green	Rank	Interaction Map	description	network_comparison	Network Comparison Type	red
378.206	147	High confidence	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	1.29455	Divided	292.152
	307			86.054	Subtracted
379.277	55	Low confidence	selenoprotein t. [swissprot;acc:q9nzj3]	2.17326	Divided	174.52
	275			204.757	Subtracted
379.474	148	High confidence	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	1.29435	Divided	293.178
	149		cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
	305		cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	86.296	Subtracted
	306		cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
384.407	62		dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	1.82385	Divided	210.767
	187			173.64	Subtracted
384.733	186		glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	1.22228	Divided	470.251
	311			85.518	Subtracted
384.843	295		adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	1.10902	Divided	426.8
	378			41.957	Subtracted
385.626	66		soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	1.78524	Divided	688.436
	73	Low confidence
	104	High confidence		302.81	Subtracted
	194	Low confidence
391	128		double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563]	1.32993	Divided	294
	443			97	Subtracted
399.534	233	High confidence	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	1.14538	Divided	348.823
	360			50.711	Subtracted
402	100		atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	1.47761	Divided	594
	171			192	Subtracted
402.138	520	Low confidence	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	1.05585	Divided	380.866
	735			21.272	Subtracted
403.196	48	High confidence	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	2.15895	Divided	870.482
	61			467.286	Subtracted
405.367	385		40s ribosomal protein s28. [swissprot;acc:p25112]	1.04615	Divided	387.486
	430			17.881	Subtracted
410	115	Low confidence	g protein-coupled receptor kinase grk5 (ec 2.7.1.-) (g-protein-coupled receptor kinase 5). [swissprot;acc:p34947]	1.3561	Divided	556
	116		g protein-coupled receptor kinase grk6 (ec 2.7.1.-) (g-protein-coupled receptor kinase 6). [swissprot;acc:p43250]
	335		g protein-coupled receptor kinase grk5 (ec 2.7.1.-) (g-protein-coupled receptor kinase 5). [swissprot;acc:p34947]	146	Subtracted
	336		g protein-coupled receptor kinase grk6 (ec 2.7.1.-) (g-protein-coupled receptor kinase 6). [swissprot;acc:p43250]
416.524	77	High confidence	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	1.70956	Divided	712.071
	106			295.547	Subtracted
417.983	167		transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	1.26047	Divided	331.61
	303			86.373	Subtracted
420.355	168		transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	1.2585	Divided	334.012
	304			86.343	Subtracted
421	108		basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	1.44178	Divided	292
	245			129	Subtracted
426.641	340	Low confidence	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	1.13821	Divided	374.834
	596			51.807	Subtracted
429	477	High confidence	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1.00704	Divided	426
	479			3	Subtracted
	791	Low confidence		1.00704	Divided
	811			3	Subtracted
430.121	145		lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	1.28761	Divided	553.827
	390			123.706	Subtracted

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.