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	Network Comparison Type	Value Type	Interaction Map	red	Filtered	green	network_comparison

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Showing element 51 to 100 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Divided	Ranked	High confidence	15	28	1.86667
		Subtracted	Squared		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
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Divided	Measured	Low confidence	2399.5	543.5	4.4149
			Squared		1362.75	69.9153	19.4914
			Rooted		48.9847	23.3131	2.10117
		Subtracted	Ranked		223	330	107
			Rooted		48.9847	23.3131	25.6716
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Squared		332411	473408	140997
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		Ranked	High confidence	337	232	105
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Rooted		145.551	168.796	23.245
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]			Low confidence	202.235	178.965	23.27
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Measured	High confidence	41482.5	33356.5	8126
	cytohesin 4. [swissprot;acc:q9uia0]	Divided	Ranked		15	28	1.86667
		Subtracted	Squared		407289	263351	143938
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	Measured		1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		Ranked	Low confidence	223	330	1.47982
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Measured		736.5	2113.5	2.86965
			Squared		128.386	1057.25	8.23493
			Rooted		27.1385	45.9728	1.69401
		Subtracted	Ranked		318	240	78
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Squared		332411	473408	140997
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Measured		36469.3	43503.3	7034
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		Ranked	High confidence	212	309	97
6	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Rooted	Low confidence	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]	Divided	Ranked	High confidence	15	28	1.86667
		Subtracted	Squared		407289	263351	143938
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]			Low confidence	299771	424645	124874
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	Measured	High confidence	1153.5	339.5	3.39764
			Squared		314.926	27.2805	11.544
			Rooted		33.9632	18.4255	1.84327
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	Measured	Low confidence	36360.3	43368.8	7008.5
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Divided			736.5	2113.5	2.86965
			Squared		128.386	1057.25	8.23493
			Rooted		27.1385	45.9728	1.69401
		Subtracted	Ranked		318	240	78
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Divided					1.325
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Subtracted	Rooted	High confidence	145.551	168.796	23.245
	protein x 0004. [refseq;acc:nm_016301]		Ranked		212	309	97
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		Measured		44490.5	36927.5	7563
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]				21185	28492	7307
			Squared	Low confidence	106226	192141	85915
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	Ranked	High confidence	215	322	1.49767
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	Rooted	Low confidence	145.551	168.796	23.245

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.