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	Filtered	red	green	network_comparison

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Showing element 2414 to 2463 of 3228 in total

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

Rank	description	red	green	network_comparison
2414	alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443]	6956.32	7223.14	1.03836
2415	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	6956.62	7223.09	1.0383
2416	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	8048.38	7752.09	1.03822
2417	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	3598.55	3467.65	1.03775
2418	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	4857.03	5039.78	1.03763
2419	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
2420	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]
2421	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	7355.46	7088.93	1.0376
2422	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]
2423	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
2424	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
2425	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]
2426	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [swissprot;acc:q01658]	6123.47	6351.84	1.03729
2427	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	5333.6	5531.41	1.03709
2428	fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116]	7243.19	7509.81	1.03681
2429	fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114]
2430	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7243.07	7509.58	1.0368
2431	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787]	7242.75	7508.98	1.03676
2432	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	8154.48	8453.84	1.03671
2433	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9]	4585.86	4753.26	1.0365
2434	wd repeat domain 26. [refseq;acc:nm_025160]	6423.46	6655.9	1.03619
2435	activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	3669.33	3797.78	1.03501
2436	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	3708.67	3584.47	1.03465
2437	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
2438	rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701]	7139.06	7384.85	1.03443
2439	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	3754.39	3629.51	1.03441
2440	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	4730.66	4891.26	1.03395
2441	adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677]	6477.82	6695.58	1.03362
2442	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]	5454.62	5637.88	1.0336
2443	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	3634.59	3756.67	1.03359
2444	adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2]	6478.14	6695.67	1.03358
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	3754.96	1.03353
2446	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	4031.94	4166.99	1.0335
2447	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	3730.53	3611.05	1.03309
2448	40s ribosomal protein s16. [swissprot;acc:p17008]
2449	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	3730.74	3611.45	1.03303
2450	pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177]	6737.15	6957.34	1.03268
2451	2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
2452	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	6042.36	6237.19	1.03224
2453	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	6931.15	7152.73	1.03197
2454	homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	8751.01	8480.03	1.03196
2455	prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	5978.83	6166.89	1.03145
2456	pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399]
2457	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	4998.72	5155.87	1.03144
2458	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	4751.74	4900.37	1.03128
2459	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
2460	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
2461	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	5114.15	5272.92	1.03105
2462	bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
2463	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234]

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.