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 1530 to 1579 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
765	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
776	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Divided	225.996	215.535	1.04854
	sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900]	Subtracted	221.965	212.404	9.561
777	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Divided	225.989	215.53	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	221.965	212.404	9.561
778	beta-catenin (pro2286). [swissprot;acc:p35222]		224.445	214.894	9.551
	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Divided	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
	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Subtracted	231.734	222.222	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	232.762	243.933	1.04799
	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Subtracted	231.734	222.222	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	245.84	257.636	1.04798
782	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Subtracted	231.734	222.222	9.512
	translin. [swissprot;acc:q15631]	Divided	224.385	235.131	1.04789
783	60s ribosomal protein l8. [swissprot;acc:p25120]	Subtracted	231.734	222.222	9.512
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	Divided	224.385	235.131	1.04789
784	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Subtracted	231.734	222.222	9.512
	polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]	Divided	224.385	235.131	1.04789
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
	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Subtracted	231.734	222.222	9.512
786	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]
	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]	Divided	244.447	233.508	1.04685
787	down-regulated in metastasis. [refseq;acc:nm_014503]
	rw1 protein (fragment). [swissprot;acc:q92545]	Subtracted	231.734	222.222	9.512
788	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Divided	138.705	132.538	1.04653
	loh1cr12. [refseq;acc:nm_058169]	Subtracted	230.087	220.579	9.508
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]	Divided	224.244	234.511	1.04578
	unr protein. [swissprot;acc:o75534]	Subtracted	230.087	220.579	9.508
790	40s ribosomal protein s21. [swissprot;acc:p35265]	Divided	224.244	234.511	1.04578

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.