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 1501 to 1550 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
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
	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	Divided	229.045	218.343	1.04901
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]		213.804	224.226	1.04875
	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Subtracted	209.191	219.332	10.141
767	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]		228.563	238.668	10.105
	rho interacting protein 3. [refseq;acc:nm_015134]	Divided	213.803	224.224	1.04874
768	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	1.04873
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Subtracted	213.325	203.303	10.022
769	cab2. [refseq;acc:nm_033419]	Divided	210.946	221.225	1.04873
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Subtracted	213.256	203.237	10.019
770	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]	Divided	210.946	221.225	1.04873
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	59	49	10
771	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]	Divided	210.946	221.225	1.04873
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	59	49	10
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	Divided	210.946	221.225	1.04873
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Subtracted	59	49	10
773	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	Divided	210.946	221.225	1.04873
774	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	Subtracted	221.716	231.501	9.785
	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	Divided	225.996	215.535	1.04854
775	histone deacetylase 2 (hd2). [swissprot;acc:q92769]		226.003	215.541
	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	Subtracted	221.676	231.453	9.777

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.