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

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Showing element 3180 to 3228 of 3228 in total

Value Type  : Measured
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]	1200	6465.72	5950.27	1.08663
yeast sec31p homolog. [refseq;acc:nm_014933]	774	6533.36	5874.76	1.11211
yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470]	1127	6303.92	5790.65	1.08864
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906]	2397	6970.07	6707.29	1.03918
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	2457	5155.87	4998.72	1.03144
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24]	708	5944.25	5317.78	1.11781
zasp protein (fragment). [sptrembl;acc:q9y4z3]	1464	6103.49	5671.93	1.07609
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]	1252	9340.98	8618.32	1.08385
zinc finger imprinted 2. [swissprot;acc:q9nzv7]	2484	3675.97	3568.45	1.03013
zinc finger protein 174 (aw-1). [swissprot;acc:q15697]	2485	3675.65	3568.18	1.03012
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022]	2483	3676.38	3568.8	1.03014
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	1782	5744.89	5386.37	1.06656
zinc finger protein 207. [swissprot;acc:o43670]	1169	5949.49	5470.44	1.08757
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771]	2482	3676.61	3568.99	1.03015
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	2481	3676.39	3568.8
zinc finger protein 232. [swissprot;acc:q9uny5]	2478	3676.57	3568.96
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	2477	3676.43	3568.84
zinc finger protein 258. [refseq;acc:nm_145310]	1775	5744.89	5386.37	1.06656
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	1776
zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	1777
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6]	2476	3676.7	3569.07	1.03016
zinc finger protein 277. [swissprot;acc:q9nrm2]	1625	4392.15	4102.1	1.07071
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78]	2572	7194.87	7056.42	1.01962
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]	1822	5997	5633.44	1.06454
zinc finger protein 291. [swissprot;acc:q9by12]	2230	3484.94	3650.8	1.04759
zinc finger protein 305. [swissprot;acc:o43309]	2480	3676.56	3568.95	1.03015
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]	695	8647.74	7725.1	1.11943
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337]	2475	3682.14	3573.66	1.03036
zinc finger protein 99. [refseq;acc:nm_032164]	2479	3676.6	3568.99	1.03015
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]	1184	4776.19	4392.63	1.08732
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]	1189
zinc finger protein gli3. [swissprot;acc:p10071]	1186
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	1636	9251.16	9899.73	1.07011
zinc finger protein t86. [swissprot;acc:o00488]	546	4612.54	4052.77	1.13812
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915]	1420	6096.21	5658.51	1.07735
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	1432	6095.62	5658.58	1.07723
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	1427	6095.85	5658.55	1.07728
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1]	1358	6103.54	5657.71	1.0788
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]	2106	7295.24	6916.14	1.05481
zinc finger-like protein 9. [refseq;acc:nm_033414]	452	4315.06	3760.8	1.14738
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	2656	4226.86	4191.15	1.00852
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]	1734	6272.26	5874.83	1.06765
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]	833	4965.35	4489.72	1.10594
[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]	934	6195.52	5640	1.0985
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118]	925	6193.07	5637.43	1.09856
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119]	926	6193.08	5637.45

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.