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

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Showing element 51 to 100 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Value Type	Interaction Map	green	network_comparison	red
4	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Divided	Ranked	High confidence	28	1.86667	15
		Subtracted	Squared		263351	143938	407289
	cytohesin 4. [swissprot;acc:q9uia0]		Measured		33356.5	8126	41482.5
	hbs1-like. [refseq;acc:nm_006620]	Divided			698.5	3.71868	2597.5
			Squared		115.48	13.8285	1596.92
			Rooted		26.4292	1.92839	50.9657
		Subtracted				24.5365
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]	Divided	Measured	Low confidence	543.5	4.4149	2399.5
			Squared		69.9153	19.4914	1362.75
			Rooted		23.3131	2.10117	48.9847
		Subtracted	Ranked		330	107	223
			Rooted		23.3131	25.6716	48.9847
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Squared		473408	140997	332411
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]		Ranked	High confidence	232	105	337
5	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Rooted		168.796	23.245	145.551
	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]			Low confidence	178.965	23.27	202.235
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]		Measured	High confidence	33356.5	8126	41482.5
	cytohesin 4. [swissprot;acc:q9uia0]	Divided	Ranked		28	1.86667	15
		Subtracted	Squared		263351	143938	407289
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Divided	Measured		339.5	3.39764	1153.5
			Squared		27.2805	11.544	314.926
			Rooted		18.4255	1.84327	33.9632
	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473]		Ranked	Low confidence	330	1.47982	223
	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3]		Measured		2113.5	2.86965	736.5
			Squared		1057.25	8.23493	128.386
			Rooted		45.9728	1.69401	27.1385
		Subtracted	Ranked		240	78	318
	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Squared		473408	140997	332411
	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Measured		43503.3	7034	36469.3
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		Ranked	High confidence	309	97	212
6	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]		Rooted	Low confidence	168.796	23.245	145.551
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Divided	Ranked	High confidence	28	1.86667	15
		Subtracted	Squared		263351	143938	407289
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]			Low confidence	424645	124874	299771
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]	Divided	Measured	High confidence	339.5	3.39764	1153.5
			Squared		27.2805	11.544	314.926
			Rooted		18.4255	1.84327	33.9632
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	Measured	Low confidence	43368.8	7008.5	36360.3
	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5]	Divided			2113.5	2.86965	736.5
			Squared		1057.25	8.23493	128.386
			Rooted		45.9728	1.69401	27.1385
		Subtracted	Ranked		240	78	318
	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	168.796	23.245	145.551
	protein x 0004. [refseq;acc:nm_016301]		Ranked		309	97	212
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]		Measured		36927.5	7563	44490.5
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]				28492	7307	21185
			Squared	Low confidence	192141	85915	106226
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Divided	Ranked	High confidence	322	1.49767	215
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted	Rooted	Low confidence	168.796	23.245	145.551

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.