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

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Showing element 501 to 550 of 77072 in total

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green	Rank	Interaction Map	Value Type	network_comparison	description	Network Comparison Type	red
5.39669	42	High confidence	Squared	6.23345	nanos (fragment). [sptrembl;acc:q8wy41]	Divided	33.64
	52			4.39835	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]		1.22698
	56	Low confidence
	358	High confidence		28.2433	nanos (fragment). [sptrembl;acc:q8wy41]	Subtracted	33.64
	420			4.16971	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]		1.22698
	774	Low confidence
5.42219	90			2.32179	lats homolog 1. [refseq;acc:nm_004690]	Divided	12.5892
	91	High confidence
		Low confidence			sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
	92	High confidence
	400			7.16701	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	Low confidence			lats homolog 1. [refseq;acc:nm_004690]
	762				sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
5.56738	10		Measured	35.8425	serpin b12. [swissprot;acc:q96p63]	Divided	199.549
	11	High confidence
	168			193.982		Subtracted
	280	Low confidence
5.56776	544		Rooted	1.04727	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]	Divided	5.83095
	768			0.26319		Subtracted
5.58446	61		Squared	4.12898	laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]	Divided	23.0581
	732			17.4736		Subtracted
5.66499	43	High confidence	Rooted	1.75134	40s ribosomal protein s26. [swissprot;acc:p02383]	Divided	9.92134
	115			4.25635		Subtracted
5.71669	11	Low confidence	Measured	34.8539	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Divided	199.249
	12	High confidence
	169			193.532		Subtracted
	281	Low confidence
5.76	21	High confidence	Squared	243.36	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]	Divided	0.0236686
	407			5.73633		Subtracted
5.80317	15	Low confidence		207.905	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]	Divided	0.0279126
	766			5.77526		Subtracted
5.80678	32		Rooted	1.69589	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Divided	9.84765
	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]
	196			4.04087	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.