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

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Showing element 662 to 711 of 3228 in total

Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1

green	Rank	description	red	network_comparison
3611.05	2447	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	3730.53	1.03309
	2448	40s ribosomal protein s16. [swissprot;acc:p17008]
3611.45	2449	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	3730.74	1.03303
3629.51	2439	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	3754.39	1.03441
3652.28	2321	dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9]	3496.21	1.04464
3675.65	2485	zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	3568.18	1.03012
3675.97	2484	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	3568.45	1.03013
3676.38	2483	zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	3568.8	1.03014
3676.39	2481	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]		1.03015
3676.43	2477	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	3568.84
3676.56	2480	zinc finger protein 305. [swissprot;acc:o43309]	3568.95
3676.57	2478	zinc finger protein 232. [swissprot;acc:q9uny5]	3568.96
3676.6	2479	zinc finger protein 99. [refseq;acc:nm_032164]	3568.99
3676.61	2482	zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]
3676.7	2476	zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6]	3569.07	1.03016
3682.14	2475	zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337]	3573.66	1.03036
3682.72	2360	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	3843.06	1.04354
3688.96	2634	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	3640.58	1.01329
3705.05	2500	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	3804.53	1.02685
3710.01	2523	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	3803.04	1.02508
3718.86	2539	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	3805.17	1.02321
3734.8	2486	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	3626.38	1.0299
3754.96	2445	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	3633.14	1.03353
3755.33	2220	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	3936.2	1.04816
3755.5	2221	thrombospondin 3 precursor. [swissprot;acc:p49746]	3936.33	1.04815
3756.67	2443	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	3634.59	1.03359
3759.28	2533	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	3847.84	1.02356
3762.56	317	adiponectin receptor 2. [refseq;acc:nm_024551]	3153.1	1.19329
3775.86	2553	ras-related protein rab-37. [swissprot;acc:q96ax2]	3852.99	1.02043
	2554	ras-related protein rab-26. [swissprot;acc:q9ulw5]
	2555	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
3788.42	2530	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	3880.5	1.02431
3797.78	2435	activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	3669.33	1.03501
3804.85	2308	60s ribosomal protein l7. [swissprot;acc:p18124]	3976.92	1.04522
3816.38	2376	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	3976.48	1.04195
3818.01	2377	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	3977.7	1.04183
3818.09	2378	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	3977.76	1.04182
3819.84	2379	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	3979.06	1.04168
3829.53	2582	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	3899.28	1.01821
3857.88	2583	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	3926.4	1.01776
3870.8	273	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	3199.4	1.20985
3877.14	2628	40s ribosomal protein s9. [swissprot;acc:p46781]	3933.74	1.0146
3888.18	199	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	4916.8	1.26455
3897.1	97	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	2820.51	1.3817
3928.38	2630	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	3985.17	1.01446
3947.54	2633	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	4000.73	1.01347
3972.32	2685	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	3953.53	1.00475
	2686	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
	2687	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]
	2688	oligophrenin 1. [swissprot;acc:o60890]

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.