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	Hugo	description	Network Comparison Type	Value Type	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 2214 to 2263 of 3228 in total

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

Rank	Hugo	description	red	network_comparison	green
2214	FABP4	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090]	221.509	1.00637	220.108
2215	no value	fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469]
2216	FABP7	fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]
2217	WDR4	wd-repeat protein 4. [swissprot;acc:p57081]
2218	PMP2	myelin p2 protein. [swissprot;acc:p02689]
2219	KLHL8	kelch-like protein 8. [swissprot;acc:q9p2g9]
2220	PNMT	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
2221	no value	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
2222	BCMO1	beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]
2223	FABP3	fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]
2224	RPE65	retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]
2225	INMT	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	CFL1	cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528]	217.955	1.00634	219.336
2227	CFL2	cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
2228	FDXR	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570]	211.81		213.153
2229	DSTN	destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282]	217.955		219.336
2230	UFD1L	ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890]
2231	SYVN1	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	221.842	1.00633	223.246
2232	RAPSN	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	TRIM3	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	202.414	1.00631	203.691
2234	no value	seven in absentia homolog 1. [refseq;acc:nm_003031]	223.608	1.00625	225.005
2235	RARS2	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	200.95	1.0062	199.711
2236	no value	protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981]	222.959	1.00618	224.337
2237	BRD3	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	222.965		224.343
2238	BRD4	bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]	222.959		224.337
2239	BRDT	testis-specific bromodomain protein. [refseq;acc:nm_001726]	222.958		224.336
2240	LRRC4	nag14 protein. [refseq;acc:nm_022143]	222.959		224.337
2241	BRD2	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	222.96		224.338
2242	ITM2B	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	209.197	1.00617	207.915
2243	ITM2C	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
2244	ITM2A	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
2245	FBLN2	fibulin-2 precursor. [swissprot;acc:p98095]	191.618	1.00614	190.448
2246	MRPL18	mitochondrial ribosomal protein l18. [refseq;acc:nm_014161]	223.58	1.0061	224.943
2247	ADI1	sipl protein. [refseq;acc:nm_018269]	208.609	1.00609	207.346
2248	KIF3C	kinesin-like protein kif3c. [swissprot;acc:o14782]	219.045	1.00608	220.377
2249	PC	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	181.091	1.00607	179.999
2250	CSTF2T	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	164.064	1.00606	165.058
2251	ENOPH1	e-1 enzyme. [refseq;acc:nm_021204]	208.315		207.061
2252	ALAD	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	217.185	1.00605	218.498
2253	KIF3B	kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066]	219.047	1.00604	220.371
2254	no value	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	ZFHX3	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	202.366	1.00595	203.57
2256	SIAH2	seven in absentia homolog 2. [refseq;acc:nm_005067]	223.546	1.00592	224.869
2257	QPRT	nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274]	212.563	1.00591	211.315
2258	CDC37	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	223.888	1.00582	225.191
2259	DMC1	meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565]	213.391	1.00569	214.606
2260	TSEN34	leng5 protein. [refseq;acc:nm_024075]	221.599	1.00566	220.351
2261	WARS	tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]
2262	no value	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]
2263	WARS2	tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]

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
- Hugo is the HGNC identifier if it exists
- 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.