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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 3180 to 3228 of 3228 in total

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

description	Rank	green	red	network_comparison
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108]	2476	210.577	211.205	1.00298
yeast sec31p homolog. [refseq;acc:nm_014933]	1136	212.675	218.484	1.02731
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470]	1955	213.703	211.633	1.00978
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	1639	197.364	194.516	1.01464
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	528	237.393	222.146	1.06864
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	1626	214.2	217.446	1.01515
zasp protein (fragment). [sptrembl;acc:q9y4z3]	1992	217.207	219.267	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	190.909	191.936	1.00538
zinc finger imprinted 2. [swissprot;acc:q9nzv7]	1063	278.232	269.96	1.03064
zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	1062	278.239	269.963	1.03066
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	1066	278.223	269.956	1.03062
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	2630	225.195	224.891	1.00135
zinc finger protein 207. [swissprot;acc:o43670]	1633	218.658	221.934	1.01498
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]	1072	278.217	269.954	1.03061
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	1067	278.223	269.956	1.03062
zinc finger protein 232. [swissprot;acc:q9uny5]	1069	278.218	269.954	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	278.221	269.955	1.03062
zinc finger protein 258. [refseq;acc:nm_145310]	2622	225.195	224.891	1.00135
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	2623
zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	2624
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6]	1068	278.215	269.953	1.03061
zinc finger protein 277. [swissprot;acc:q9nrm2]	1087	243.679	236.679	1.02958
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78]	2444	206.753	206.086	1.00324
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	2126	222.788	221.248	1.00696
zinc finger protein 291. [swissprot;acc:q9by12]	350	265.696	242.14	1.09728
zinc finger protein 305. [swissprot;acc:o43309]	1065	278.219	269.954	1.03062
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	1487	203.989	207.877	1.01906
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337]	1080	278.093	269.896	1.03037
zinc finger protein 99. [refseq;acc:nm_032164]	1070	278.218	269.954	1.03061
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]	2466	235.088	235.812	1.00308
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]	2471
zinc finger protein gli3. [swissprot;acc:p10071]	2468
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	1557	192.996	196.192	1.01656
zinc finger protein t86. [swissprot;acc:o00488]	579	231.796	246.805	1.06475
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	1348	213.832	218.569	1.02215
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	1350	213.847	218.574	1.0221
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	1349	213.841	218.572	1.02212
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]	1327	213.648	218.509	1.02275
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	2190	208.162	209.54	1.00662
zinc finger-like protein 9. [refseq;acc:nm_033414]	532	235.004	250.942	1.06782
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	580	252.038	236.751	1.06457
zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5]	2822	0.00001	0.00001	1
zinc transporter 3 (znt-3). [swissprot;acc:q99726]	3049
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]	2435	218.117	217.366	1.00346
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]	960	229.677	237.558	1.03431
[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]	1518	209.524	213.259	1.01783
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	1507	209.5	213.274	1.01801
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]	1508

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.