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

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Showing element 501 to 550 of 77072 in total

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green	red	description	network_comparison	Value Type	Interaction Map	Network Comparison Type	Rank
5.39669	1.22698	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	4.16971	Squared	High confidence	Subtracted	420
					Low confidence		774
			4.39835		High confidence	Divided	52
					Low confidence		56
	33.64	nanos (fragment). [sptrembl;acc:q8wy41]	6.23345		High confidence		42
			28.2433			Subtracted	358
5.42219	12.5892	lats homolog 1. [refseq;acc:nm_004690]	2.32179			Divided	91
					Low confidence		90
			7.16701		High confidence	Subtracted	400
					Low confidence		761
		sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	2.32179		High confidence	Divided	92
					Low confidence		91
			7.16701		High confidence	Subtracted	401
					Low confidence		762
5.56738	199.549	serpin b12. [swissprot;acc:q96p63]	35.8425	Measured	High confidence	Divided	11
					Low confidence		10
			193.982		High confidence	Subtracted	168
					Low confidence		280
5.56776	5.83095	adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]	0.26319	Rooted			768
			1.04727			Divided	544
5.58446	23.0581	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	4.12898	Squared			61
			17.4736			Subtracted	732
5.66499	9.92134	40s ribosomal protein s26. [swissprot;acc:p02383]	1.75134	Rooted	High confidence	Divided	43
			4.25635			Subtracted	115
5.71669	199.249	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	34.8539	Measured		Divided	12
					Low confidence		11
			193.532		High confidence	Subtracted	169
					Low confidence		281
5.76	0.0236686	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]	5.73633	Squared	High confidence		407
			243.36			Divided	21
5.80317	0.0279126	fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]	5.77526		Low confidence	Subtracted	766
			207.905			Divided	15
5.80678	9.84765	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	1.69589	Rooted			36
			4.04087			Subtracted	200
		melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	1.69589			Divided	32
			4.04087			Subtracted	196
		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1.69589			Divided	45
			4.04087			Subtracted	208
		melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	1.69589			Divided	34
			4.04087			Subtracted	198
		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	1.69589			Divided	44
			4.04087			Subtracted	207
		melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	1.69589			Divided	35
			4.04087			Subtracted	199
		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	1.69589			Divided	33
			4.04087			Subtracted	197
		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	1.69589			Divided	40
			4.04087			Subtracted	203
		melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	1.69589			Divided	37
			4.04087			Subtracted	201

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.