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

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Showing element 1625 to 1674 of 3228 in total

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

green	Rank	description	red	network_comparison
6092.77	2113	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251]	5776.79	1.0547
6092.93	2247	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	5819.36	1.04701
6093.56	1439	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	5658.8	1.07683
6093.65	2117	ataxin 2-binding protein. [swissprot;acc:q9nwb1]	5778.16	1.0546
6094.89	2089	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	5775.22	1.05535
6095.62	1432	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	5658.58	1.07723
6095.85	1427	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	5658.55	1.07728
6096.21	1420	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	5658.51	1.07735
6103.49	1464	zasp protein (fragment). [sptrembl;acc:q9y4z3]	5671.93	1.07609
6103.52	1360	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]	5657.72	1.07879
	1361	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8]
6103.54	1357	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	5657.71	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]
6103.57	1356	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805]		1.07881
6103.92	1463	collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955]	5672.2	1.07611
6103.98	1457	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	5672.23	1.07612
6103.99	1462	transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472]	5672.24
6104.01	1456	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	5672.25
	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]
6104.26	1814	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	5733.71	1.06463
6104.68	1455	lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457]	5672.68	1.07615
6106.48	2248	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	5833.01	1.04688
6108.72	1837	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	5739.49	1.06433
	1838	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
	1839	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]
6109.31	381	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	5246.01	1.16456
6111.8	1329	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]	5656.82	1.08043
6111.84	1328	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]	5656.81	1.08044
6111.9	1327	p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671]	5656.8	1.08045
6112.02	1325	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]	5656.79	1.08047
6113.01	2252	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161]	5840.54	1.04665
6113.35	940	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	5568.96	1.09775
6113.79	1848	heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900]	5746.06	1.064
6113.96	2519	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741]	5964.17	1.02511
	2520	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
	2521	17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034]
	2522	retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725]
6119.36	1465	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]	5686.74	1.07608
6120.62	1298	sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5]	5655.85	1.08218
6120.64	1286	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928]
	1287	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477]
	1288	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]
	1289	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]
	1290	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]
	1291	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]
	1292	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]
	1293	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]

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.