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

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Showing element 3075 to 3124 of 14920 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	Value Type	description	Filtered	red	green	network_comparison
385	Ranked	testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]	0	10302.7	10686.7	1.03727
		transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	1	266.421	244.236	1.09083
	Squared	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]		15043.7	18560.1	1.23375
		lamin b2. [swissprot;acc:q03252]	0	539.519	494.357	1.09136
	Rooted	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	1	50.7723	46.0607	1.10229
		histone deacetylase 2 (hd2). [swissprot;acc:q92769]	0	30.7569	31.8678	1.03612
386	Measured	60s ribosomal protein l8. [swissprot;acc:p25120]	1	4533.74	5279.4	1.16447
		pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	0	2156.64	2254.12	1.0452
	Ranked	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	1	242.238	264.11	1.09029
		testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	0	10303.7	10687.4	1.03724
	Squared	mesoderm induction early response 1. [refseq;acc:nm_020948]		958.952	880.365	1.08927
		scratch; scratch 1. [refseq;acc:nm_031309]	1	40388.9	49827.5	1.23369
	Rooted	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	0	39.0883	37.7357	1.03584
		protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1	50.0513	45.4124	1.10215
387	Measured	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	0	1388.29	1330.37	1.04354
		hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	1	4533.74	5279.4	1.16447
	Ranked	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]		242.238	264.11	1.09029
		thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	0	10481.8	10869.5	1.03699
	Squared	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	1	15053	18568	1.23351
		nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	0	12.0783	13.1443	1.08826
	Rooted	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	1	50.3345	45.6718	1.10209
		likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	0	29.6492	28.6255	1.03576
388	Measured	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	1	4533.74	5279.4	1.16447
		scratch; scratch 1. [refseq;acc:nm_031309]	0	1398.21	1339.9	1.04352
	Ranked	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]		9953.39	10320.9	1.03692
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1	227.575	208.756	1.09015
	Squared	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		40315.7	49716.4	1.23318
		putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	0	948.513	872.867	1.08666
	Rooted	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]		34.4922	35.713	1.03539
		serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	1	50.3345	45.6718	1.10209
389	Measured	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	0	11512.3	12011.7	1.04338
		probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	1	4533.74	5279.4	1.16447
	Ranked	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	0	11794.7	11375.4	1.03686
		small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	1	227.575	208.756	1.09015
	Squared	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]		31819.7	39222.2	1.23264
		likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	0	605.501	557.57	1.08596
	Rooted	60s ribosomal protein l34. [swissprot;acc:p49207]	1	50.3345	45.6718	1.10209
		intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	0	30.454	29.4181	1.03521
390	Measured	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]		11512.3	12011.7	1.04338
		rw1 protein (fragment). [swissprot;acc:q92545]	1	4533.74	5279.4	1.16447
	Ranked	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]		241.828	263.62	1.09011
		alpha-nac protein. [sptrembl;acc:q9h009]	0	14204.4	14724.5	1.03662
	Squared			12.1126	13.1421	1.08499
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	1	28895.6	35572.8	1.23108
	Rooted	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]		50.3345	45.6718	1.10209
		williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	0	7.21166	7.46223	1.03475
391	Measured	seven in absentia homolog 1. [refseq;acc:nm_003031]		2221.04	2316.94	1.04318
		tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	1	3658.76	3144.39	1.16358
	Ranked	40s ribosomal protein s16. [swissprot;acc:p17008]		241.828	263.62	1.09011
		nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	0	14223.9	14738.5	1.03618

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.