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

Results: HTML CSV LaTeX

Showing element 1650 to 1699 of 3228 in total

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

red	Rank	green	description	network_comparison
5655.85	1298	6120.62	sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5]	1.08218
5656.79	1325	6112.02	serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209]	1.08047
5656.8	1327	6111.9	p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671]	1.08045
5656.81	1328	6111.84	serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299]	1.08044
5656.82	1329	6111.8	serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454]	1.08043
5657.53	824	6263.02	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	1.10702
	825		atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]
5657.71	1356	6103.57	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805]	1.07881
	1357	6103.54	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	1.0788
	1358		zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]
	1359		dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
5657.72	1360	6103.52	calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206]	1.07879
	1361		calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]
5658.51	1420	6096.21	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	1.07735
5658.55	1427	6095.85	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	1.07728
5658.58	1432	6095.62	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	1.07723
5658.8	1439	6093.56	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	1.07683
5659.22	1478	6084.68	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	1.07518
5659.45	1471	6087.55	40s ribosomal protein s8. [swissprot;acc:p09058]	1.07564
5660.17	1480	6085.22	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	1.07509
5665.34	1596	6070.32	enigma protein; lim domain protein. [refseq;acc:nm_005451]	1.07148
	1597		eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]
5666.91	2307	5923.48	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	1.04528
5669.9	1939	6015.75	brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728]	1.061
5671.62	2010	6003.67	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	1.05855
5671.93	1464	6103.49	zasp protein (fragment). [sptrembl;acc:q9y4z3]	1.07609
5672.2	1463	6103.92	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	1.07611
5672.23	1457	6103.98	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	1.07612
5672.24	1462	6103.99	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]
5672.25	1456	6104.01	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]
	1458		mitochondrial ribosomal protein l24. [refseq;acc:nm_024540]
	1459		65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
	1461		9 kda protein. [swissprot;acc:p13994]
5672.68	1455	6104.68	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	1.07615
5675.96	1312	6136.47	u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579]	1.08113
5678.02	1230	6161.65	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	1.08518
5680.76	999	6220.45	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098]	1.095
	1000		ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]
	1001		lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]
	1002		seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]
	1003		seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]
5682	2395	5905.08	homeobox protein otx2. [swissprot;acc:p32243]	1.03926
5683.17	1746	6065.55	regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127]	1.06728
5684.61	2007	6018.72	adaptor-related protein complex 1, mu 1 subunit (mu-adaptin 1) (adaptor protein complex ap-1 mu-1 subunit) (golgi adaptor ha1/ap1 adaptin mu-1 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 1) (clathrin coat assembly protein ap47) (clathrin coat associated protein ap47) (ap-mu chain family member mu1a). [swissprot;acc:q9bxs5]	1.05877
5685.08	1270	6156.48	epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772]	1.08292
5685.34	1261	6157.53	epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929]	1.08305
5685.38	1259	6157.7	epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204]	1.08308
5685.77	1315	6145.43	dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098]	1.08084
5686.74	1465	6119.36	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]	1.07608
5691.1	2399	5913.92	homeobox protein otx1. [swissprot;acc:p32242]	1.03915

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.