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

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green	network_comparison	red	Rank	description	Value Type	Network Comparison Type	Interaction Map
5.39669	4.16971	1.22698	420	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Squared	Subtracted	High confidence
			774				Low confidence
	4.39835		52			Divided	High confidence
			56				Low confidence
	6.23345	33.64	42	nanos (fragment). [sptrembl;acc:q8wy41]			High confidence
	28.2433		358			Subtracted
5.42219	2.32179	12.5892	90	lats homolog 1. [refseq;acc:nm_004690]		Divided	Low confidence
			91				High confidence
				sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]			Low confidence
			92				High confidence
	7.16701		400	lats homolog 1. [refseq;acc:nm_004690]		Subtracted
			401	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
			761	lats homolog 1. [refseq;acc:nm_004690]			Low confidence
			762	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
5.56738	35.8425	199.549	10	serpin b12. [swissprot;acc:q96p63]	Measured	Divided
			11				High confidence
	193.982		168			Subtracted
			280				Low confidence
5.56776	0.26319	5.83095	768	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]	Rooted
	1.04727		544			Divided
5.58446	4.12898	23.0581	61	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	Squared
	17.4736		732			Subtracted
5.66499	1.75134	9.92134	43	40s ribosomal protein s26. [swissprot;acc:p02383]	Rooted	Divided	High confidence
	4.25635		115			Subtracted
5.71669	34.8539	199.249	11	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Measured	Divided	Low confidence
			12				High confidence
	193.532		169			Subtracted
			281				Low confidence
5.76	5.73633	0.0236686	407	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]	Squared		High confidence
	243.36		21			Divided
5.80317	5.77526	0.0279126	766	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]		Subtracted	Low confidence
	207.905		15			Divided
5.80678	1.69589	9.84765	32	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted
			33	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
			34	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
			35	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
			36	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
			37	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
			39	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
			40	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
			41	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
			42	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
			43	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
			44	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
			45	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
			47	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
			48	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
	4.04087		196	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]		Subtracted
			197	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
			198	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]

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.