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 718 to 767 of 3228 in total

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

Rank	description	red	green	network_comparison
718	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	223.121	211.685	1.05402
719	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	247.769	235.074	1.054
720	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	231.92	244.435	1.05396
721	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	214.765	203.8	1.0538
722	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	217.952	206.902	1.05341
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	244.842	232.577	1.05274
724	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
725	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	235.296	247.673	1.0526
726	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	244.495	232.419	1.05196
727	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	208.873	219.71	1.05188
728	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]	208.874	219.708	1.05187
729	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]
730	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]
731	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]
732	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	124.434	118.318	1.05169
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	164	155.961	1.05154
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	232.601	244.534	1.0513
735	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
736	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
737	septin 10 isoform 1. [refseq;acc:nm_144710]	125.526	119.402	1.05129
738	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	222.825	211.966	1.05123
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	223.58	235.027	1.0512
740	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]
741	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]
742	brain protein 44. [swissprot;acc:o95563]	126.215	120.078	1.05111
743	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]
744	septin 6. [swissprot;acc:q14141]	126.604	120.463	1.05098
745	solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	214.679	225.568	1.05072
746	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	250.465	238.38	1.0507
747	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
748	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	245.246	233.483	1.05038
749	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	221.968	211.326	1.05036
750	exocyst complex component sec15a. [swissprot;acc:q8tag9]	222.138	211.503	1.05028
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	223.463	212.875	1.04974
752	step ii splicing factor slu7. [refseq;acc:nm_006425]
753	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	224.434	235.583	1.04968
754	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
755	uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172]
756	cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
757	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]
758	phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]
759	osteoclast stimulating factor 1. [swissprot;acc:q92882]	231.809	243.289	1.04952
760	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	246.055	234.458	1.04946
761	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	213.325	203.303	1.0493
762	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	213.256	203.237
763	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	228.78	218.091	1.04901
764	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	222.082	211.707
765	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	229.045	218.343
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	213.804	224.226	1.04875
767	rho interacting protein 3. [refseq;acc:nm_015134]	213.803	224.224	1.04874

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.