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 2230 to 2279 of 3228 in total

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

Rank	description	red	green	network_comparison
2230	zinc finger protein 291. [swissprot;acc:q9by12]	3650.8	3484.94	1.04759
2231	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
2232	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]
2233	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	3614.08	3450.07	1.04754
2234	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	3614.07
2235	40s ribosomal protein s3. [swissprot;acc:p23396]	3674.29	3508.13	1.04736
2236	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023]	5902.27	6181.21	1.04726
2237	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]	5902.26
2238	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]	5902.27
2239	sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637]
2240	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]
2241	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	3670.45	3504.91	1.04723
2242	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
2243	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	5776.96	6049.61	1.0472
2244	gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915]
2245	inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839]
2246	dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	6209.77	6501.99	1.04706
2247	rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062]	5819.36	6092.93	1.04701
2248	signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624]	5833.01	6106.48	1.04688
2249	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	6834.03	7153.66	1.04677
2250	esterase d (ec 3.1.1.1). [swissprot;acc:p10768]
2251	serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270]	6196.65	6486.12	1.04671
2252	arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161]	5840.54	6113.01	1.04665
2253	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	3629.21	3467.48	1.04664
2254	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	7383.13	7727.39	1.04663
2255	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	3624.59	3463.37	1.04655
2256	ubiquitin. [swissprot;acc:p02248]	7390.36	7733.85	1.04648
2257	sr rich protein. [refseq;acc:nm_032870]	6245.32	6534.23	1.04626
2258	60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]	5150.31	5388.05	1.04616
2259	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	6486.84	6786.23	1.04615
2260	block 23. [sptrembl;acc:q8nhw5]	5150.14	5387.84
2261	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	6486.84	6786.23
2262	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	5148.88	5386.34	1.04612
2263	40s ribosomal protein s3a. [swissprot;acc:p49241]	4918.64	5145.39	1.0461
2264	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	3633.74	3473.68	1.04608
2265	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	3612.45	3453.39	1.04606
2266	transcription factor iib. [refseq;acc:nm_013242]	9146.11	8743.98	1.04599
2267	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]
2268	eyes absent homolog 1. [swissprot;acc:q99502]	5785.08	6051.03	1.04597
2269	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	6373.94	6666.87	1.04596
2270	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	6568.41	6869.9	1.0459
2271	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	6568.51	6869.97	1.04589
2272	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
2273	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	6374.64	6667.06	1.04587
2274	eyes absent homolog 3. [swissprot;acc:q99504]	5779.66	6044.78
2275	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	6570.74	6872.1	1.04586
2276	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	5783.69	6048.87	1.04585
2277	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	5783.72	6048.9
2278	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]	5783.76	6048.94
2279	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]	5783.73	6048.91

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.