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	network_comparison	green

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Showing element 2213 to 2262 of 3228 in total

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

Rank	description	red	network_comparison	green
2213	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	210.127	1.00642	211.475
2214	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090]	221.509	1.00637	220.108
2215	fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469]
2216	fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]
2217	wd-repeat protein 4. [swissprot;acc:p57081]
2218	myelin p2 protein. [swissprot;acc:p02689]
2219	kelch-like protein 8. [swissprot;acc:q9p2g9]
2220	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
2221	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
2222	beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]
2223	fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]
2224	retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]
2225	indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050]
2226	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	217.955	1.00634	219.336
2227	cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
2228	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	211.81		213.153
2229	destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]	217.955		219.336
2230	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
2231	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	221.842	1.00633	223.246
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	1.00632	214.194
2233	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	202.414	1.00631	203.691
2234	seven in absentia homolog 1. [refseq;acc:nm_003031]	223.608	1.00625	225.005
2235	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	200.95	1.0062	199.711
2236	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	222.959	1.00618	224.337
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	1.00617	207.915
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	1.00614	190.448
2246	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	223.58	1.0061	224.943
2247	sipl protein. [refseq;acc:nm_018269]	208.609	1.00609	207.346
2248	kinesin-like protein kif3c. [swissprot;acc:o14782]	219.045	1.00608	220.377
2249	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	181.091	1.00607	179.999
2250	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	164.064	1.00606	165.058
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	1.00605	218.498
2253	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066]	219.047	1.00604	220.371
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	1.00598	194.22
2255	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	202.366	1.00595	203.57
2256	seven in absentia homolog 2. [refseq;acc:nm_005067]	223.546	1.00592	224.869
2257	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	212.563	1.00591	211.315
2258	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	223.888	1.00582	225.191
2259	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	213.391	1.00569	214.606
2260	leng5 protein. [refseq;acc:nm_024075]	221.599	1.00566	220.351
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]

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.