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

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Showing element 59824 to 59873 of 77072 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
3067	retinoic acid receptor rxr-beta. [swissprot;acc:p28702]	Measured	Subtracted	High confidence	0	0	0
		Ranked	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Squared	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Rooted	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]		Divided	Low confidence	72.8776	75.2083	1.03198
	u5 snrnp-specific protein; u5 snrnp-specific protein (220 kd), ortholog of s. cerevisiae prp8p; precursor mrna processing protein; splicing factor prp8. [refseq;acc:nm_006445]		Subtracted		72.301	74.5976	2.2966
3068	chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	Measured			8064.98	8285.76	220.78
	eyes absent homolog 1. [swissprot;acc:q99502]	Rooted	Divided		71.33	73.6113	1.03198
	gamma-tubulin complex component 5 (gcp-5). [swissprot;acc:q96rt8]	Ranked	Subtracted		200.314	197.051	3.263
	headcase homolog; hhdc for homolog of drosophila headcase. [refseq;acc:nm_016217]	Measured	Divided	High confidence	0.00001	0.00001	1
			Subtracted		0	0	0
		Ranked	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Squared	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Rooted	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Squared	Divided	Low confidence	45741.3	44186	1.0352
	probable cation-transporting atpase 2 (ec 3.6.3.-) (cgi-152). [swissprot;acc:q9hd20]	Measured			8056.09	8280.14	1.02781
	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	Squared	Subtracted		45663.6	44150.2	1513.4
	snare protein ykt6; ykt6, s. cerevisiae, homolog of. [refseq;acc:nm_006555]	Ranked	Divided		201.754	198.467	1.01656
	translocation protein sec63 homolog. [swissprot;acc:q9ugp8]	Rooted	Subtracted		70.584	72.8806	2.2966
3069	40s ribosomal protein s10. [swissprot;acc:p46783]	Measured	Divided		8010.65	8233.31	1.0278
	bone morphogenetic protein 5 precursor (bmp-5). [swissprot;acc:p22003]			High confidence	0.00001	0.00001	1
			Subtracted		0	0	0
		Ranked	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Squared	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Rooted	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
	g protein beta subunit-like. [refseq;acc:nm_022372]	Ranked		Low confidence	200.202	196.94	3.262
	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	Rooted	Divided		72.0816	74.3867	1.03198
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]		Subtracted		71.2037	73.5002	2.2965
	poly(rc)-binding protein 3 (alpha-cp3). [swissprot;acc:p57721]	Measured			7827.31	8048.03	220.72
	signal transducer and activator of transcription 3 (acute-phase response factor). [swissprot;acc:p40763]	Squared	Divided		42501.8	41056.5	1.0352
	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]		Subtracted		45166.2	43653.1	1513.1
	voltage-dependent anion-selective channel protein 3 (vdac-3) (hvdac3) (outer mitochondrial membrane protein porin 3). [swissprot;acc:q9y277]	Ranked	Divided		198.825	195.586	1.01656
3070	chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	Measured	Subtracted		8065.18	8285.87	220.69
	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]		Divided		8074.27	8298.71	1.0278
	g protein beta subunit-like. [refseq;acc:nm_022372]	Squared			46615.9	45030.7	1.0352
	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	Ranked			201.449	198.168	1.01656
	mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [refseq;acc:nm_153487]	Measured		High confidence	0.00001	0.00001	1
			Subtracted		0	0	0
		Ranked	Divided		0.00001	0.00001	1
			Subtracted		0	0	0
		Squared	Divided		0.00001	0.00001	1

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.