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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 1518 to 1567 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
759	osteoclast stimulating factor 1. [swissprot;acc:q92882]	Divided	243.289	231.809	1.04952
760	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]	Subtracted	234.511	224.244	10.267
	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	Divided	234.458	246.055	1.04946
761	serpin b11. [swissprot;acc:q96p15]	Subtracted	234.511	224.244	10.267
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Divided	203.303	213.325	1.0493
762	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]		203.237	213.256
	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	Subtracted	234.511	224.244	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	218.091	228.78	1.04901
764	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]	Subtracted	234.511	224.244	10.267
	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	Divided	211.707	222.082	1.04901
765	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	Subtracted	232.805	243.067	10.262
	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	Divided	218.343	229.045	1.04901
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]		224.226	213.804	1.04875
	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Subtracted	219.332	209.191	10.141
767	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]		238.668	228.563	10.105
	rho interacting protein 3. [refseq;acc:nm_015134]	Divided	224.224	213.803	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]		221.225	210.946	1.04873
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Subtracted	203.303	213.325	10.022
769	cab2. [refseq;acc:nm_033419]	Divided	221.225	210.946	1.04873
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Subtracted	203.237	213.256	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	221.225	210.946	1.04873
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	49	59	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	221.225	210.946	1.04873
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	49	59	10
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	Divided	221.225	210.946	1.04873
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Subtracted	49	59	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	221.225	210.946	1.04873
774	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	Subtracted	231.501	221.716	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	215.535	225.996	1.04854
775	histone deacetylase 2 (hd2). [swissprot;acc:q92769]		215.541	226.003
	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	Subtracted	231.453	221.676	9.777
776	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Divided	215.535	225.996	1.04854
	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	Subtracted	212.404	221.965	9.561
777	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Divided	215.53	225.989	1.04853
	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]	Subtracted	212.404	221.965	9.561
778	beta-catenin (pro2286). [swissprot;acc:p35222]		214.894	224.445	9.551
	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Divided	219.332	209.191	1.04848
779	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]		241.641	230.516	1.04826
	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Subtracted	222.222	231.734	9.512
780	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	Divided	243.933	232.762	1.04799
	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Subtracted	222.222	231.734	9.512
781	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	Divided	257.636	245.84	1.04798
782	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Subtracted	222.222	231.734	9.512
	translin. [swissprot;acc:q15631]	Divided	235.131	224.385	1.04789
783	60s ribosomal protein l8. [swissprot;acc:p25120]	Subtracted	222.222	231.734	9.512
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	Divided	235.131	224.385	1.04789
784	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Subtracted	222.222	231.734	9.512

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.