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

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Showing element 451 to 500 of 77072 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided

Rank	description	Interaction Map	network_comparison	green	red
226	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	High confidence	1.15165	758.411	658.544
	zinc finger protein 33a (zinc finger protein kox31) (ha0946). [swissprot;acc:q06730]	Low confidence	1.19451	1968.69	2351.62
227	similar to zinc finger protein 91 (hpf7, htf10) (fragment). [sptrembl;acc:q86w65]		1.1945	1968.91	2351.86
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	High confidence	1.14972	369.011	424.258
228	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]		1.14835	4696.36	4089.65
	zinc finger protein 234 (zinc finger protein hzf4) (fragment). [swissprot;acc:q14588]	Low confidence	1.1945	1968.83	2351.77
229	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	High confidence	1.14829	368.317	320.752
	zinc finger protein 41. [swissprot;acc:p51814]	Low confidence	1.1945	1968.87	2351.81
230	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	High confidence	1.14713	1718.6	1498.17
	zinc finger protein 300. [swissprot;acc:q96re9]	Low confidence	1.1945	1968.91	2351.86
231	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	High confidence	1.14705	1759.22	2017.91
	zinc finger protein zfp31 (fragment). [sptrembl;acc:q92971]	Low confidence	1.1945	1968.91	2351.86
232	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	High confidence	1.14579	1906.28	1663.73
	zinc finger protein 286. [swissprot;acc:q9hbt8]	Low confidence	1.19449	1969.01	2351.96
233	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	High confidence	1.14538	399.534	348.823
	zinc finger protein 7 (zinc finger protein kox4) (zinc finger protein hf.16). [swissprot;acc:p17097]	Low confidence	1.19449	1969.01	2351.96
234	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	High confidence	1.14333	4550.64	5202.89
	zinc finger protein 304. [swissprot;acc:q9hcx3]	Low confidence	1.19449	1969.05	2352.01
235	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	High confidence	1.14326	1843.92	1612.86
	zinc finger protein 83 (zinc finger protein hpf1). [swissprot;acc:p51522]	Low confidence	1.19449	1968.97	2351.92
236	f23269_2. [sptrembl;acc:o75290]		1.19448	1969.11	2352.07
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	High confidence	1.1426	3103.01	2715.75
237	dj54b20.4 (novel krab box containing c2h2 type zinc finger protein). [sptrembl;acc:q96qh7]	Low confidence	1.19448	1969.25	2352.23
	p28 ing5. [refseq;acc:nm_032329]	High confidence	1.13707	2243.69	2551.23
238	casein kinase i alpha s-like. [refseq;acc:nm_145203]		1.13678	1933.94	2198.47
	zinc finger protein 415. [refseq;acc:nm_018355]	Low confidence	1.19448	1969.15	2352.12
239	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	High confidence	1.13666	434.366	382.142
	zinc finger protein 35 (zinc finger protein hf.10). [swissprot;acc:p13682]	Low confidence	1.19448	1969.29	2352.27
240	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	High confidence	1.13575	1676.18	1475.83
	zinc finger protein 10 (zinc finger protein kox1) (fragment). [swissprot;acc:p21506]	Low confidence	1.19448	1969.19	2352.16
241	keratin associated protein 9.2. [refseq;acc:nm_031961]	High confidence	1.13574	1079.01	1225.47
	zinc finger protein 225. [swissprot;acc:q9uk10]	Low confidence	1.19448	1969.19	2352.16
242	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	High confidence	1.13524	642.343	729.216
	zinc finger protein 256 (bone marrow zinc finger 3) (bmzf-3). [swissprot;acc:q9y2p7]	Low confidence	1.19448	1969.19	2352.16
243	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	High confidence	1.13502	1079.36	1225.09
	zinc finger protein 214 (bwscr2 associated zinc-finger protein 1) (baz 1). [swissprot;acc:q9ul59]	Low confidence	1.19448	1969.19	2352.16
244	dj54b20.2 (novel krab box containing c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q96qh9]			1969.25	2352.23
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	High confidence	1.13502	1079.36	1225.09
245	keratin associated protein 1.5. [refseq;acc:nm_031957]
	zinc finger protein 165 (ld65). [swissprot;acc:p49910]	Low confidence	1.19448	1969.19	2352.16
246	ba526d8.4 (novel krab box containing c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q9h559]			1969.25	2352.23
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	High confidence	1.13502	1079.36	1225.09
247	dj153g14.3 (novel c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q9ujn7]	Low confidence	1.19448	1969.11	2352.07
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	High confidence	1.13502	1079.36	1225.09
248	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]		1.135	1079.37
	zinc finger protein 264. [swissprot;acc:o43296]	Low confidence	1.19448	1969.15	2352.12
249	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	High confidence	1.135	1079.37	1225.08
	zinc finger protein 228. [swissprot;acc:q9uju3]	Low confidence	1.19448	1969.25	2352.23
250	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	High confidence	1.135	1079.37	1225.08
	zinc finger protein 224. [swissprot;acc:q9nzl3]	Low confidence	1.19447	1969.49	2352.49

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.