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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 77072 in total

Rank	Filtered	description	green	Value Type	Network Comparison Type	red	Interaction Map	network_comparison
2	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	23.3131	Rooted	Divided	48.9847	Low confidence	2.10117
					Subtracted			25.6716
			69.9153	Squared	Divided	1362.75		19.4914
			330	Ranked	Subtracted	223		107
			543.5	Measured	Divided	2399.5		4.4149
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5		Subtracted	41482.5	High confidence	8126
		hbs1-like. [refseq;acc:nm_006620]	322	Ranked		215		107
		lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	330		Divided	223	Low confidence	1.47982
		mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	28			15	High confidence	1.86667
			263351	Squared	Subtracted	407289		143938
		rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	Rooted	Divided	21.225		2.30547
					Subtracted			27.7086
			1357.07	Squared	Divided	48.0356		28.2513
			2394.5	Measured		450.5		5.31521
3	0	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	Rooted	Subtracted	36.9188		30.0631
		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	66			45.6289	Low confidence	20.3711
		apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628	Squared		135280	High confidence	35348
		cab2. [refseq;acc:nm_033419]	10950	Ranked		21866		10916
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	1.87479	Squared	Divided	0.00001	Low confidence	187479
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	9.43398	Rooted				943398
			89	Measured				8900000
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	20617	Ranked		9607		2.14604
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]			Subtracted			11010
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9		Divided	4475.84	High confidence	2.47638
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Measured	Subtracted	23818.1		4196.8
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75			5106.93	Low confidence	2393.82
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109		Divided	0.00001	High confidence	10900000
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	197937	Squared	Subtracted	220988	Low confidence	23051
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001		Divided	5.61325	High confidence	561325
				Rooted		12.4097		1240970
	1	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]	330	Ranked		223	Low confidence	1.47982
		cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534]	23.3131	Rooted		48.9847		2.10117
					Subtracted			25.6716
			69.9153	Squared	Divided	1362.75		19.4914
			330	Ranked	Subtracted	223		107
			543.5	Measured	Divided	2399.5		4.4149
		cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	Ranked		15	High confidence	1.86667
			263351	Squared	Subtracted	407289		143938
		cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	33356.5	Measured		41482.5		8126
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	Rooted	Divided	50.9657		1.92839
					Subtracted			24.5365
			115.48	Squared	Divided	1596.92		13.8285
			698.5	Measured		2597.5		3.71868
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	28492		Subtracted	21185	Low confidence	7307
		rad50-interacting protein 1. [refseq;acc:nm_021930]	232	Ranked		337	High confidence	105
		vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]	475045	Squared		333506	Low confidence	141539
4	0	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	4356	Measured		2082		2274
		cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954]	295570	Squared		273831		21739
		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	0.823905		Divided	0.00001		82390.5
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	9.43398	Rooted				943398

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.