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 762 to 811 of 3228 in total

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

Rank	description	red	green	network_comparison
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	1.0493
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
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
769	cab2. [refseq;acc:nm_033419]
770	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]
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]
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]
773	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]
774	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	1.04854
775	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	226.003	215.541
776	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	225.996	215.535
777	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	225.989	215.53	1.04853
778	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	209.191	219.332	1.04848
779	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	230.516	241.641	1.04826
780	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	232.762	243.933	1.04799
781	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	245.84	257.636	1.04798
782	translin. [swissprot;acc:q15631]	224.385	235.131	1.04789
783	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]
784	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
785	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863]	244.447	233.508	1.04685
786	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555]
787	down-regulated in metastasis. [refseq;acc:nm_014503]
788	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	138.705	132.538	1.04653
789	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	1.04578
790	40s ribosomal protein s21. [swissprot;acc:p35265]
791	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]
792	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
793	bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]
794	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]
795	serpin b11. [swissprot;acc:q96p15]
796	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]
797	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
798	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]
799	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	221.965	212.404	1.04501
800	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
801	beta-catenin (pro2286). [swissprot;acc:p35222]	224.445	214.894	1.04445
802	testis-specific protein tex28. [swissprot;acc:o15482]	212.386	221.785	1.04425
803	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]
804	a kindred of iglon. [refseq;acc:nm_173808]
805	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]
806	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]
807	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]
808	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
809	syntaxin 16 (syn16). [swissprot;acc:o14662]
810	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
811	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]

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.