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 2208 to 2257 of 3228 in total

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

Rank	description	red	green	network_comparison
2208	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]	199.129	200.413	1.00645
2209	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]
2210	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]
2211	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]
2212	28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3]	224.411	225.854	1.00643
2213	dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475]	210.127	211.475	1.00642
2214	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090]	221.509	220.108	1.00637
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	219.336	1.00634
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	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

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.