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	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 6308 to 6357 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	green	network_comparison
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	2708	Subtracted	1	188.435	188.31	0.125
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	203		0	12196.2	11009.7	1186.5
	219	Divided				1.10777
	1180	Subtracted	1	210.986	216.344	5.358
	1201	Divided				1.0254
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	1209			207.931	213.175	1.02522
	1231	Subtracted				5.244
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]	1018			211.908	218.627	6.719
	1028	Divided				1.03171
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597]	1017	Subtracted				6.719
	1027	Divided				1.03171
suppressor of actin 1. [refseq;acc:nm_014016]	91	Subtracted	0	19088.1	16804.6	2283.5
	173	Divided				1.13589
	2826		1	0.00001	0.00001	1
		Subtracted		0	0	0
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	754			210.946	221.225	10.279
	773	Divided				1.04873
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	1322	Subtracted		216.542	211.908	4.634
	1372	Divided				1.02187
suppressor of fused. [refseq;acc:nm_016169]	2432	Subtracted		235.812	235.088	0.724
	2467	Divided				1.00308
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	430	Subtracted		250.938	234.134	16.804
	496	Divided				1.07177
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	196		0	11064.2	9897.84	1.11784
	207	Subtracted				1166.36
	290		1	242.109	264.79	22.681
	380	Divided				1.09368
suppressor of var1, 3-like 1. [refseq;acc:nm_003171]	2184			211.713	210.318	1.00663
	2188	Subtracted				1.395
surfeit locus protein 1. [swissprot;acc:q15526]	1512	Divided		213.268	209.509	1.01794
	1522	Subtracted				3.759
surfeit locus protein 5. [swissprot;acc:q15528]	260			242.14	265.696	23.556
	349	Divided				1.09728
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	479	Subtracted	0	13236.8	13159.3	77.5
	487	Divided				1.00589
	1619	Subtracted	1	228.496	231.729	3.233
	1668	Divided				1.01415
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]	1625	Subtracted				3.233
	1674	Divided				1.01415
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	1168	Subtracted		219.03	213.604	5.426
	1200	Divided				1.0254
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	489	Subtracted	0	6802.96	6829.74	26.78
	492	Divided				1.00394
	2496	Subtracted	1	234.384	234.948	0.564
	2514	Divided				1.00241
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	2589	Subtracted		220.02	219.696	0.324
	2592	Divided				1.00147
swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074]	2567	Subtracted		220.016	219.667	0.349
	2574	Divided				1.00159
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075]	347	Subtracted	0	13247.9	12674.2	573.7

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.