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

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Showing element 501 to 550 of 77072 in total

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