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	Rank	network_comparison	Interaction Map	red	description

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Showing element 951 to 1000 of 77072 in total

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

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.