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

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Showing element 3150 to 3199 of 3228 in total

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

description	Rank	red	green	network_comparison
wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	1407	206.104	210.424	1.02096
wd repeat domain 26. [refseq;acc:nm_025160]	1429	213.351	217.74	1.02057
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	1410	206.1	210.417	1.02095
wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	2927	0.00001	0.00001	1
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	507	251.299	234.729	1.07059
wd-repeat protein 3. [swissprot;acc:q9unx4]	912	243.896	234.96	1.03803
wd-repeat protein 4. [swissprot;acc:p57081]	2217	221.509	220.108	1.00637
wd-repeat protein bing4. [swissprot;acc:o15213]	1008	243.227	235.475	1.03292
wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	853	108.289	112.772	1.0414
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135]	1325	217.133	212.289	1.02282
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	1876	223.862	226.271	1.01076
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	1875
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	3218	0.00001	0.00001	1
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	1874	223.862	226.271	1.01076
wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	2625	204.304	204.028	1.00135
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]	546	207.222	194.262	1.06671
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]	1975	214.611	212.546	1.00972
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]	1973
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	1974
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	825	206.214	197.614	1.04352
wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882]	3109	0.00001	0.00001	1
wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]	3065
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312]	1537	228.419	232.376	1.01732
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	1073	216.901	210.485	1.03048
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]	2882	0.00001	0.00001	1
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]	1685	216.899	213.889	1.01407
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	856	215.028	206.623	1.04068
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	9	212	309	1.45755
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	738	222.825	211.966	1.05123
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385]	2328	209.326	208.357	1.00465
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	2476	211.205	210.577	1.00298
yeast sec31p homolog. [refseq;acc:nm_014933]	1136	218.484	212.675	1.02731
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470]	1955	211.633	213.703	1.00978
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	1639	194.516	197.364	1.01464
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	528	222.146	237.393	1.06864
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	1626	217.446	214.2	1.01515
zasp protein (fragment). [sptrembl;acc:q9y4z3]	1992	219.267	217.207	1.00948
zinc finger daz interacting protein 1. [refseq;acc:nm_014934]	2981	0.00001	0.00001	1
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315]	2278	191.936	190.909	1.00538
zinc finger imprinted 2. [swissprot;acc:q9nzv7]	1063	269.96	278.232	1.03064
zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	1062	269.963	278.239	1.03066
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	1066	269.956	278.223	1.03062
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	2630	224.891	225.195	1.00135
zinc finger protein 207. [swissprot;acc:o43670]	1633	221.934	218.658	1.01498
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]	1072	269.954	278.217	1.03061
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	1067	269.956	278.223	1.03062
zinc finger protein 232. [swissprot;acc:q9uny5]	1069	269.954	278.218	1.03061
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	1064	269.955	278.221	1.03062
zinc finger protein 258. [refseq;acc:nm_145310]	2622	224.891	225.195	1.00135
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	2623

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.