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	network_comparison	green

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Showing element 713 to 762 of 3228 in total

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

Rank	description	red	network_comparison	green
713	dendritic cell protein. [refseq;acc:nm_006360]	223.121	1.05402	211.685
714	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]
715	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
716	cpz gene product. [refseq;acc:nm_003652]
717	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
718	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]
719	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	247.769	1.054	235.074
720	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	231.92	1.05396	244.435
721	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	214.765	1.0538	203.8
722	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	217.952	1.05341	206.902
723	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	244.842	1.05274	232.577
724	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
725	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	235.296	1.0526	247.673
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	1.05196	232.419
727	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	208.873	1.05188	219.71
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	1.05187	219.708
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	1.05169	118.318
733	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	164	1.05154	155.961
734	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	232.601	1.0513	244.534
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	1.05129	119.402
738	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	222.825	1.05123	211.966
739	phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067]	223.58	1.0512	235.027
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	1.05111	120.078
743	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]
744	septin 6. [swissprot;acc:q14141]	126.604	1.05098	120.463
745	solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	214.679	1.05072	225.568
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	1.0507	238.38
747	trinucleotide repeat containing 15. [refseq;acc:nm_015575]
748	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	245.246	1.05038	233.483
749	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	221.968	1.05036	211.326
750	exocyst complex component sec15a. [swissprot;acc:q8tag9]	222.138	1.05028	211.503
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	223.463	1.04974	212.875
752	step ii splicing factor slu7. [refseq;acc:nm_006425]
753	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	224.434	1.04968	235.583
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	1.04952	243.289
760	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	246.055	1.04946	234.458
761	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	213.325	1.0493	203.303
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

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.