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	Interaction Map	Gene	Rank	description	Filtered	Network Comparison Type	red	network_comparison

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Showing element 644 to 693 of 3228 in total

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

green	Rank	description	red	network_comparison
3504.91	2242	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	3670.45	1.04723
3508.13	2235	40s ribosomal protein s3. [swissprot;acc:p23396]	3674.29	1.04736
3516.98	2343	40s ribosomal protein s5. [swissprot;acc:p46782]	3672.17	1.04413
3520.86	2374	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	3669.57	1.04224
3521.41	2381	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	3667.94	1.04161
3526.65	2372	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	3677.53	1.04278
	2373	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
3529.35	2386	60s ribosomal protein l30. [swissprot;acc:p04645]	3674.02	1.04099
3531.96	2491	hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	3436.65	1.02773
	2492	growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]
	2493	growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
	2494	hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]
	2495	growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293]
3543.33	2380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	3690.79	1.04162
3569.68	2385	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	3716.43	1.04111
3580.35	2225	60s ribosomal protein l9. [swissprot;acc:p32969]	3750.99	1.04766
3584.47	2436	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	3708.67	1.03465
	2437	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
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

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.