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	red	Filtered	green	network_comparison

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Showing element 51 to 100 of 66312 in total

Filtered  : 1

Rank	description	Value Type	Network Comparison Type	Interaction Map	red	green	network_comparison
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Ranked	Divided	High confidence	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
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Measured	Divided	Low confidence	2399.5	543.5	4.4149
		Ranked	Subtracted		223	330	107
		Squared	Divided		1362.75	69.9153	19.4914
		Rooted			48.9847	23.3131	2.10117
			Subtracted				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]	Ranked	Divided		15	28	1.86667
		Squared	Subtracted		407289	263351	143938
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Measured	Divided		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
		Ranked	Subtracted		318	240	78
		Squared	Divided		128.386	1057.25	8.23493
		Rooted			27.1385	45.9728	1.69401
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]	Squared	Subtracted		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]	Ranked	Divided	High confidence	15	28	1.86667
		Squared	Subtracted		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]	Measured	Divided	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]	Measured	Subtracted	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
		Ranked	Subtracted		318	240	78
		Squared	Divided		128.386	1057.25	8.23493
		Rooted			27.1385	45.9728	1.69401
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]	Ranked			318	240	1.325
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Rooted	Subtracted	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]	Ranked	Divided	High confidence	215	322	1.49767
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	Subtracted	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.