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 1580 to 1629 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
790	testis-specific protein tex28. [swissprot;acc:o15482]	Subtracted	212.386	221.785	9.399
791	cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453]	Divided	224.244	234.511	1.04578
	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]	Subtracted	212.386	221.785	9.399
792	a kindred of iglon. [refseq;acc:nm_173808]
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Divided	224.244	234.511	1.04578
793	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]	Subtracted	212.386	221.785	9.399
	bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595]	Divided	224.244	234.511	1.04578
794	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]	Subtracted	212.386	221.785	9.399
	plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120]	Divided	224.244	234.511	1.04578
795	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	Subtracted	212.386	221.785	9.399
	serpin b11. [swissprot;acc:q96p15]	Divided	224.244	234.511	1.04578
796	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]	Subtracted	212.386	221.785	9.399
	placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237]	Divided	224.244	234.511	1.04578
797	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
	syntaxin 16 (syn16). [swissprot;acc:o14662]	Subtracted	212.386	221.785	9.399
798	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
	leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740]	Divided	224.244	234.511	1.04578
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
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Subtracted	212.386	221.785	9.399
800	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
	nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]	Divided	221.965	212.404	1.04501
801	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]	Subtracted	212.386	221.785	9.399
	beta-catenin (pro2286). [swissprot;acc:p35222]	Divided	224.445	214.894	1.04445
802	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Subtracted	212.386	221.785	9.399
	testis-specific protein tex28. [swissprot;acc:o15482]	Divided			1.04425
803	similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61]
	syntaxin 1b. [swissprot;acc:q15531]	Subtracted			9.399
804	a kindred of iglon. [refseq;acc:nm_173808]	Divided			1.04425
	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	Subtracted			9.399
805	ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]	Divided			1.04425
	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]	Subtracted			9.399
806	inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]	Divided			1.04425
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Subtracted	267.447	276.773	9.326
807	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	Divided	212.386	221.785	1.04425
	trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102]	Subtracted	218.521	227.796	9.275
808	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]		223.186	213.912	9.274
	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]	Divided	212.386	221.785	1.04425
809	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	Subtracted	233.298	242.571	9.273
	syntaxin 16 (syn16). [swissprot;acc:o14662]	Divided	212.386	221.785	1.04425
810	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	Subtracted	240.194	230.957	9.237
811	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Divided	212.386	221.785	1.04425
812	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
	putatative 28 kda protein. [refseq;acc:nm_020143]	Subtracted	227.241	236.467	9.226
813	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]	Divided	212.386	221.785	1.04425
	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	Subtracted	228.599	219.399	9.2
814	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Divided	212.386	221.785	1.04425
	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	Subtracted	244.155	234.96	9.195
815	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821]		246.354	237.223	9.131

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.