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 36 to 85 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
3	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Ranked	Divided	1	15	28	1.86667
		Squared	Subtracted		407289	263351	143938
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured			41482.5	33356.5	8126
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		Divided		2597.5	698.5	3.71868
		Squared			1596.92	115.48	13.8285
		Rooted			50.9657	26.4292	1.92839
			Subtracted				24.5365
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Ranked	Divided	0	4475.84	11083.9	2.47638
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured	Subtracted		23818.1	19621.3	4196.8
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]		Divided		0.00001	109	10900000
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Ranked	Subtracted	1	337	232	105
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	Divided	0	5.61325	0.00001	561325
		Rooted			12.4097		1240970
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked		1	15	28	1.86667
		Squared	Subtracted		407289	263351	143938
	cytohesin 4. [swissprot;acc:q9uia0]	Measured			41482.5	33356.5	8126
	hbs1-like. [refseq;acc:nm_006620]		Divided		2597.5	698.5	3.71868
		Squared			1596.92	115.48	13.8285
		Rooted			50.9657	26.4292	1.92839
			Subtracted				24.5365
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	Divided	0	0.00001	89	8900000
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked			8906	21883	2.45711
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Rooted	Subtracted		29.3087	7.61577	21.6929
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Ranked			11525	21888	10363
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Squared	Divided		0.00001	2.81207	281207
		Rooted				10.4403	1044030
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Ranked	Subtracted	1	337	232	105
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Squared		0	75446.7	105900	30453.3
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Measured			18704	21730	3026
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Rooted		1	145.551	168.796	23.245
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured			41482.5	33356.5	8126
	cytohesin 4. [swissprot;acc:q9uia0]	Ranked	Divided		15	28	1.86667
		Squared	Subtracted		407289	263351	143938
	histone h4. [swissprot;acc:p02304]	Measured		0	21773.1	24446.3	2673.2
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	Divided		0.00001	1.87479	187479
		Rooted				9.43398	943398
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured				89	8900000
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]			1	1153.5	339.5	3.39764
		Squared			314.926	27.2805	11.544
		Rooted			33.9632	18.4255	1.84327
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]		Subtracted	0	19.0788	0	19.0788
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Ranked			11525	21888	10363
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		Divided		5510.5	11965.7	2.17144
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		Subtracted	1	212	309	97
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Squared		0	75446.7	105900	30453.3
6	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]				73080.8	102814	29733.2
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Ranked	Divided	1	15	28	1.86667
		Squared	Subtracted		407289	263351	143938
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	Divided	0	0.00001	89	8900000
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared				1.87479	187479

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.