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	Gene	Network Comparison Type	network_comparison	Rank	Interaction Map	red	description

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Showing element 951 to 1000 of 77072 in total

Filtered  : 0

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

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.