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 912 to 961 of 3228 in total

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

Rank	description	red	green	network_comparison
912	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]	4982.81	5480.91	1.09996
913	ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	5768.5	6342.05	1.09943
914	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	6513.45	7161	1.09942
915	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	6289.72	6911.96	1.09893
916	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
917	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
918	scratch; scratch 1. [refseq;acc:nm_031309]	7281.6	8001.64	1.09888
919	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	5396.36	5929.41	1.09878
920	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	7273.78	7991.72	1.0987
921	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	6324.31	6948.5
922	tubulin-tyrosine ligase. [refseq;acc:nm_153712]	5511.2	6054.71	1.09862
923	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	4057.54	4457.66	1.09861
924	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	5406.5	5939.42	1.09857
925	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	5637.43	6193.07	1.09856
926	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]	5637.45	6193.08
927	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868]	5638.64	6194.22	1.09853
928	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1]	5638.46	6194.04
929	surfeit locus protein 1. [swissprot;acc:q15526]
930	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	5638.65	6194.23
931	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884]	5638.59	6194.17
932	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376]	5638.46	6194.04
933	protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887]
934	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874]	5640	6195.52	1.0985
935	neurotrimin precursor (hnt). [swissprot;acc:q9p121]	5413.63	5946.46	1.09842
936	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	5628.21	6180.37	1.09811
937	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	5859.25	6432.03	1.09776
938	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
939	nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]
940	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	5568.96	6113.35	1.09775
941	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844]	4970.21	5455.34	1.09761
942	phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205]	6597.56	7240.64	1.09747
943	gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104]	6597.98	7241	1.09746
944	beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929]
945	alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733]
946	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558]	6598.37	7241.32	1.09744
947	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	11797.1	10750.2	1.09738
948	caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210]	4633.48	5084.24	1.09728
949	apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574]
950	bystin. [swissprot;acc:q13895]	4280.99	4697.02	1.09718
951	dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326]	5364.3	5885.48	1.09716
952	putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774]
953	casein kinase i alpha s-like. [refseq;acc:nm_145203]	4906.33	5382.5	1.09705
954	casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729]
955	uridine kinase-like 1. [swissprot;acc:q9nwz5]	5548.78	6086.89	1.09698
956	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	5364.77	5884.89	1.09695
957	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	4483.26	4917.77	1.09692
958	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
959	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	4379.28	4803.59	1.09689
960	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	11773	10733.2	1.09688
961	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284]

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.