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	Rank	Gene	Interaction Map	network_comparison	description	red	Network Comparison Type

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Showing element 951 to 1000 of 77072 in total

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green	Value Type	Rank	Interaction Map	network_comparison	description	red	Network Comparison Type
12.1701	Rooted	432	High confidence	1.02772	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]	12.5074	Divided
		455		0.3373			Subtracted
12.1722		86		1.3321	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	9.13761	Divided
		89	Low confidence
		170	High confidence	3.03459			Subtracted
		272	Low confidence
12.2043		165		1.15882	transcription factor bteb4 (basic transcription element binding- protein 4) (bte-binding protein 4) (krueppel-like factor 16) (novel sp1-like zinc finger transcription factor 2) (transcription factor nslp2). [swissprot;acc:q9bxk1]	10.5317	Divided
		432		1.6726			Subtracted
12.2755		570		1.0411	amiloride-sensitive sodium channel gamma-subunit (epithelial na+ channel gamma subunit) (gamma enac) (nonvoltage-gated sodium channel 1 gamma subunit) (scneg) (gamma nach). [swissprot;acc:p51170]	11.7909	Divided
		711		0.4846			Subtracted
12.2759		569		1.04115	amiloride-sensitive cation channel 3 isoform a; testis sodium channel 1; proton-gated cation channel subunit; modulatory subunit of asic2a; amiloride-sensitive cation channel 3, testis. [refseq;acc:nm_004769]	11.7907	Divided
		710		0.4852			Subtracted
12.2882		51	High confidence	1.58009	nanos (fragment). [sptrembl;acc:q8wy41]	19.4165	Divided
		57		7.1283			Subtracted
		60		1.44818	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	8.48528	Divided
		63	Low confidence
		144	High confidence	3.80292			Subtracted
		225	Low confidence
12.2937	Squared	120	High confidence	1.90407	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	6.45653	Divided
		406		5.83717			Subtracted
12.3076	Rooted	106	Low confidence	1.27875	solute carrier family 26, member 11. [refseq;acc:nm_173626]	15.7383	Divided
		244		3.4307			Subtracted
12.3132		80		1.35362	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	16.6674	Divided
		189		4.3542			Subtracted
12.3994		498		1.05566	amiloride-sensitive sodium channel delta-subunit (epithelial na+ channel delta subunit) (delta enac) (nonvoltage-gated sodium channel 1 delta subunit) (scned) (delta nach). [swissprot;acc:p51172]	11.7456	Divided
		660		0.6538			Subtracted
12.4394		372	High confidence	1.04116	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	11.9476	Divided
		432		0.4918			Subtracted
		568	Low confidence	1.04116			Divided
		708		0.4918			Subtracted
12.4629		487	High confidence	1.0032	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	12.5028	Divided
		488		0.0399			Subtracted
12.49		22		3.94968	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]	3.16228	Divided
		34		9.32772			Subtracted
12.5026		285		1.08467	40s ribosomal protein s28. [swissprot;acc:p25112]	13.5612	Divided
		368		1.0586			Subtracted
12.5624	Squared	41		7.83299	dystrophin. [swissprot;acc:p11532]	98.4011	Divided
		290		85.8387			Subtracted
12.5698	Rooted	17	Low confidence	2.29492	ptd016 protein. [refseq;acc:nm_016125]	5.47723	Divided
		30	High confidence
			Low confidence	7.09257			Subtracted
		58	High confidence
12.6095		63		1.43581	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	18.1049	Divided
		85		5.4954			Subtracted
12.6188	Squared	99	Low confidence	2.13426	zona pellucida sperm-binding protein 3 precursor (zona pellucida glycoprotein zp3) (zona pellucida protein c) (sperm receptor) (zp3a/zp3b). [swissprot;acc:p21754]	26.9318	Divided
		744		14.313			Subtracted
12.6735	Rooted	221		1.119	alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279]	14.1816	Divided
		466		1.5081			Subtracted
12.7302	Squared	101		2.12849	b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2]	27.0961	Divided
		743		14.3659			Subtracted

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.