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	Hugo	description	Value Type	Interaction Map	Network Comparison Type	Filtered	red	green	network_comparison

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Showing element 1512 to 1561 of 6456 in total

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

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
756	RPS21	40s ribosomal protein s21. [swissprot;acc:p35265]	Subtracted	224.244	234.511	10.267
757	BPI	bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213]	Divided	224.434	235.583	1.04968
	SERPINB9	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]	Subtracted	224.244	234.511	10.267
758	no value	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
	PLTP	phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058]	Divided	224.434	235.583	1.04968
759	OSTF1	osteoclast stimulating factor 1. [swissprot;acc:q92882]		231.809	243.289	1.04952
	SERPINB10	bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]	Subtracted	224.244	234.511	10.267
760	NAT10	upf0202 protein kiaa1709. [swissprot;acc:q9h0a0]	Divided	246.055	234.458	1.04946
	SERPINB8	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
761	no value	serpin b11. [swissprot;acc:q96p15]
	CBLB	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Divided	213.325	203.303	1.0493
762	CBL	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]		213.256	203.237
	SERPINB6	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	Subtracted	224.244	234.511	10.267
763	no value	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
	N6AMT1	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5]	Divided	228.78	218.091	1.04901
764	PRPF3	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]		222.082	211.707
	SERPINB1	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]	Subtracted	224.244	234.511	10.267
765	EIF3B	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]		243.067	232.805	10.262
	HEMK1	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4]	Divided	229.045	218.343	1.04901
766	SNX6	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Subtracted	209.191	219.332	10.141
	TRIOBP	protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6]	Divided	213.804	224.226	1.04875
767	no value	rho interacting protein 3. [refseq;acc:nm_015134]		213.803	224.224	1.04874
	POLR2I	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	Subtracted	228.563	238.668	10.105
768	CBLB	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]		213.325	203.303	10.022
	DNAJB4	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]	Divided	210.946	221.225	1.04873
769	CBL	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
	PERLD1	cab2. [refseq;acc:nm_033419]	Divided	210.946	221.225	1.04873
770	DNAJB5	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]
	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Subtracted	59	49	10
771	DNAJB1	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
	RRAGC	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Subtracted	59	49	10
772	ETF1	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
	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Subtracted	59	49	10
773	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
	VPS52	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	Divided	210.946	221.225	1.04873
774	MCFD2	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
	MRPS2	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	Subtracted	221.716	231.501	9.785
775	no value	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Divided	226.003	215.541	1.04854
	IMP4	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	Subtracted	221.676	231.453	9.777
776	no value	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Divided	225.996	215.535	1.04854
	SQSTM1	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	HDAC1	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Divided	225.989	215.53	1.04853
	SCP2	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	CTNNB1	beta-catenin (pro2286). [swissprot;acc:p35222]		224.445	214.894	9.551
	SNX6	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Divided	209.191	219.332	1.04848
779	DCTD	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]		230.516	241.641	1.04826
	PARK2	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Subtracted	231.734	222.222	9.512
780	no value	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]
	POLR2F	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
781	no value	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	Subtracted	231.734	222.222	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
- Hugo is the HGNC identifier if it exists
- 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.