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 7691 to 7740 of 8289 in total

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

Rank	description	red	green	network_comparison
4463	zinc finger dhhc domain containing protein 11 (zinc finger protein 399). [swissprot;acc:q9h8x9]	7754.24	7902.99	1.01918
4464	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	7497.26	7640.97	1.01917
4465	glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]	7337	7477.68
4466	5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126]	8340.85	8500.56	1.01915
4467	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	7495.76	7639.12	1.01913
4468	homolog of yeast long chain polyunsaturated fatty acid elongatio; homolog of yeast long chain polyunsaturated fatty acid elongation enzyme 2. [refseq;acc:nm_021814]	7600.51	7745.94
4469	elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9]	7600.42	7745.77	1.01912
4470	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]	7939.47	8091.2	1.01911
4471	zinc finger dhhc domain containing protein 1 (zinc finger protein 377) (dhhc-domain-containing cysteine-rich protein 1). [swissprot;acc:q8wtx9]	7755.26	7903.37	1.0191
4472	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	7939	8090.45	1.01908
4473	syntaxin 16 (syn16). [swissprot;acc:o14662]	7955.33	8106.81	1.01904
4474	th1-like; th1 drosophila homolog; th1-like (drosophila homolog); negative elongation factor proteins c and d. [refseq;acc:nm_016397]	7962.25	8113.54	1.019
4475	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	7663.2	7808.7	1.01899
4476	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	7662.83	7808.23	1.01897
4477	carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155]	8170.81	8325.77
4478	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	7662.74	7808.11
4479	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]	8286.94	8444.09	1.01896
4480	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]
4481	60s ribosomal protein l19. [swissprot;acc:p14118]	7474.75	7616.28	1.01893
4482	methyltransferase like 2. [refseq;acc:nm_018396]	8332.65	8490.24	1.01891
4483	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	7605.06	7748.82	1.0189
4484	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	7466.32	7607.46
4485	activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	7667.47	7812.25	1.01888
4486	40s ribosomal protein s3. [swissprot;acc:p23396]	7494.6	7635.68	1.01882
4487	sialic acid synthase (n-acetylneuraminate synthase) (ec 2.5.1.56) (n- acetylneuraminic acid synthase) (n-acetylneuraminate-9-phosphate synthase) (ec 2.5.1.57) (n-acetylneuraminic acid phosphate synthase). [swissprot;acc:q9nr45]
4488	homologous to yeast nitrogen permease (candidate tumor suppressor). [refseq;acc:nm_006545]	7644.55	7788.17	1.01879
4489	serpin b12. [swissprot;acc:q96p63]	8397.58	8555.3	1.01878
4490	megsin (tp55) (serpin b7). [swissprot;acc:o75635]
4491	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
4492	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]
4493	antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
4494	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232]
4495	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]
4496	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133]
4497	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	8339.92	8496.4	1.01876
4498	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]
4499	trifunctional enzyme alpha subunit, mitochondrial precursor (tp-alpha) (78 kda gastrin-binding protein) [includes: long-chain enoyl-coa hydratase (ec 4.2.1.17); long chain 3-hydroxyacyl-coa dehydrogenase (ec 1.1.1.35)]. [swissprot;acc:p40939]
4500	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643]	7643.55	7786.88	1.01875
4501	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192]	7642.49	7785.75
4502	interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515]	8204.38	8357.76	1.01869
4503	ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170]	8303.78	8458.91	1.01868
4504	aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]	8302.46	8457.37	1.01866
4505	signal recognition particle 72 kda protein (srp72). [swissprot;acc:o76094]	8440.36	8597.21	1.01858
4506	peroxisome assembly factor-1 (paf-1) (peroxin-2) (peroxisomal membrane protein 3) (35 kda peroxisomal membrane protein). [swissprot;acc:p28328]	7630.23	7771.57	1.01852
4507	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066]	8590.09	8434.52	1.01844
4508	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]	9544.1	9372.01	1.01836
4509	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915]	8374.17	8527.79	1.01834
4510	mitochondrial ribosomal protein l46; chromosome 15 open reading frame 4. [refseq;acc:nm_022163]	7613.42	7752.89	1.01832
4511	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	8734.82	8894.81
4512	acidic 82 kda protein mrna. [refseq;acc:nm_014597]	7957.9	8103.49	1.0183

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.