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

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Showing element 1763 to 1812 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
1763	DTNA	dystrobrevin alpha (dystrobrevin-alpha). [swissprot;acc:q9y4j8]	5829.73	6218.45	1.06668
1764	SNTB1	beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884]	5829.61	6218.27	1.06667
1765	SNTB2	beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425]
1766	NIT1	nitrilase 1. [refseq;acc:nm_005600]
1767	UTRN	utrophin (dystrophin-related protein 1) (drp1) (drp). [swissprot;acc:p46939]
1768	DBT	lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial precursor (ec 2.3.1.-) (e2) (dihydrolipoamide branched chain transacylase) (bckad e2 subunit). [swissprot;acc:p11182]
1769	no value	dystrophin. [swissprot;acc:p11532]
1770	AMOT	angiomotin. [refseq;acc:nm_133265]
1771	AMOTL2	angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
1772	SNTA1	alpha-1-syntrophin (59 kda dystrophin-associated protein a1, acidic component 1) (pro-tgf-alpha cytoplasmic domain-interacting protein 1) (tacip1) (syntrophin 1). [swissprot;acc:q13424]
1773	DTNB	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	5829.51	6218.11	1.06666
1774	no value	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	5386.37	5744.89	1.06656
1775	ZMYM6	zinc finger protein 258. [refseq;acc:nm_145310]
1776	ZMYM3	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
1777	ZMYM4	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]
1778	ACTR2	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
1779	COG3	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
1780	ACTR3B	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
1781	ARPC1B	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
1782	ZMYM2	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
1783	ACTR3	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
1784	ARPC3	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
1785	NRD1	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
1786	ARPC1A	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
1787	HYAL3	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	5386.48	5744.78	1.06652
1788	ARPC5	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	5386.49	5744.76	1.06651
1789	AURKB	serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4]	5839.72	6227.33	1.06637
1790	KIF23	kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]
1791	AURKC	serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9]
1792	AURKA	serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965]
1793	CYLD	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
1794	EPN2	epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964]	5948.26	6342.84	1.06634
1795	POLR3K	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1]	5501.3	5866.02	1.0663
1796	BRPF1	tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7]	5387.64	5743.5	1.06605
1797	VARS	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640]	5096.02	5432.63
1798	SNORA7A	60s ribosomal protein l32. [swissprot;acc:p02433]	3618.02	3394.29	1.06591
1799	EIF2B2	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	5456.57	5816.14	1.0659
1800	EIF2B4	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10]	5424.3	5781.58	1.06587
1801	EPN1	epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333]	5881.33	6268.57	1.06584
1802	TYMS	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	4980.54	5307.81	1.06571
1803	no value	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
1804	SDF2	stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
1805	SDF2L1	stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
1806	PKM2	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	4783.49	5097.66	1.06568
1807	MED28	endothelial-derived gene 1. [refseq;acc:nm_025205]	6399.54	6818.17	1.06542
1808	KARS	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	4941.92	5265.09	1.06539
1809	EPN3	epsin 3. [refseq;acc:nm_017957]	5816.12	6196.21	1.06535
1810	MCC	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	6520.83	6946.75	1.06532
1811	TAF9B	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	7659.42	8156.79	1.06494
1812	SYVN1	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	5514.19	5871.64	1.06482

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.