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 1480 to 1529 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
740	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Subtracted	223.463	212.875	10.588
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]	Divided	223.58	235.027	1.0512
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Subtracted	223.463	212.875	10.588
742	brain protein 44. [swissprot;acc:o95563]	Divided	126.215	120.078	1.05111
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Subtracted	226.003	215.541	10.462
743	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]		225.996	215.535	10.461
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Divided	126.215	120.078	1.05111
744	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Subtracted	225.996	215.535	10.461
	septin 6. [swissprot;acc:q14141]	Divided	126.604	120.463	1.05098
745	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Subtracted	225.989	215.53	10.459
	solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827]	Divided	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
	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	Subtracted	213.804	224.226	10.422
747	rho interacting protein 3. [refseq;acc:nm_015134]		213.803	224.224	10.421
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Divided	250.465	238.38	1.0507
748	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]		245.246	233.483	1.05038
	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	Subtracted	222.082	211.707	10.375
749	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]		210.946	221.225	10.279
	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	Divided	221.968	211.326	1.05036
750	cab2. [refseq;acc:nm_033419]	Subtracted	210.946	221.225	10.279
	exocyst complex component sec15a. [swissprot;acc:q8tag9]	Divided	222.138	211.503	1.05028
751	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]	Subtracted	210.946	221.225	10.279
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Divided	223.463	212.875	1.04974
752	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]	Subtracted	210.946	221.225	10.279
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Divided	223.463	212.875	1.04974
753	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	Subtracted	210.946	221.225	10.279
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Divided	224.434	235.583	1.04968
754	microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	Subtracted	210.946	221.225	10.279
755	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]		224.244	234.511	10.267
	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]	Divided	224.434	235.583	1.04968
756	40s ribosomal protein s21. [swissprot;acc:p35265]	Subtracted	224.244	234.511	10.267
	cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]	Divided	224.434	235.583	1.04968
757	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]
	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]	Subtracted	224.244	234.511	10.267
758	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
	phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]	Divided	224.434	235.583	1.04968
759	bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]	Subtracted	224.244	234.511	10.267
	osteoclast stimulating factor 1. [swissprot;acc:q92882]	Divided	231.809	243.289	1.04952
760	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]	Subtracted	224.244	234.511	10.267
	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	Divided	246.055	234.458	1.04946
761	serpin b11. [swissprot;acc:q96p15]	Subtracted	224.244	234.511	10.267
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Divided	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
	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	Subtracted	224.244	234.511	10.267
763	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	Divided	228.78	218.091	1.04901
764	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]	Subtracted	224.244	234.511	10.267
	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	Divided	222.082	211.707	1.04901
765	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	Subtracted	243.067	232.805	10.262

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.