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

Rank	description	red	green	network_comparison
2230	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]	217.955	219.336	1.00634
2231	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	221.842	223.246	1.00633
2232	43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702]	215.547	214.194	1.00632
2233	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	202.414	203.691	1.00631
2234	seven in absentia homolog 1. [refseq;acc:nm_003031]	223.608	225.005	1.00625
2235	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	200.95	199.711	1.0062
2236	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	222.959	224.337	1.00618
2237	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	222.965	224.343
2238	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]	222.959	224.337
2239	testis-specific bromodomain protein. [refseq;acc:nm_001726]	222.958	224.336
2240	nag14 protein. [refseq;acc:nm_022143]	222.959	224.337
2241	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	222.96	224.338
2242	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	209.197	207.915	1.00617
2243	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
2244	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
2245	fibulin-2 precursor. [swissprot;acc:p98095]	191.618	190.448	1.00614
2246	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	223.58	224.943	1.0061
2247	sipl protein. [refseq;acc:nm_018269]	208.609	207.346	1.00609
2248	kinesin-like protein kif3c. [swissprot;acc:o14782]	219.045	220.377	1.00608
2249	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	181.091	179.999	1.00607
2250	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	164.064	165.058	1.00606
2251	e-1 enzyme. [refseq;acc:nm_021204]	208.315	207.061
2252	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	217.185	218.498	1.00605
2253	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066]	219.047	220.371	1.00604
2254	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	193.065	194.22	1.00598
2255	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	202.366	203.57	1.00595
2256	seven in absentia homolog 2. [refseq;acc:nm_005067]	223.546	224.869	1.00592
2257	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	212.563	211.315	1.00591
2258	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	223.888	225.191	1.00582
2259	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	213.391	214.606	1.00569
2260	leng5 protein. [refseq;acc:nm_024075]	221.599	220.351	1.00566
2261	tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]
2262	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
2263	tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]
2264	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]
2265	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257]	211.597	210.416	1.00561
2266	probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]
2267	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]
2268	tripartite motif protein 2. [swissprot;acc:q9c040]	202.312	203.437	1.00556
2269	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	217.419	218.627
2270	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	207.54	208.69	1.00554
2271	dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326]	216.622	215.436	1.00551
2272	putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774]
2273	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750]	213.015	211.858	1.00546
2274	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209]	213.642	214.801	1.00542
2275	dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887]	207.319	208.44	1.00541
2276	dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	216.613	215.448
2277	regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754]	191.936	190.909	1.00538
2278	zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315]
2279	transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275]

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.