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

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Showing element 1768 to 1817 of 3228 in total

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

Rank	network_comparison	red	description	green
1768	1.06667	5829.61	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]	6218.27
1769			dystrophin. [swissprot;acc:p11532]
1770			angiomotin. [refseq;acc:nm_133265]
1771			angiomotin like 2; leman coiled-coil protein; angiomotin-like protein 2. [refseq;acc:nm_016201]
1772			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	1.06666	5829.51	dystrobrevin beta (beta-dystrobrevin) (dtn-b). [swissprot;acc:o60941]	6218.11
1774	1.06656	5386.37	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	5744.89
1775			zinc finger protein 258. [refseq;acc:nm_145310]
1776			zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]
1777			zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]
1778			actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
1779			conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
1780			similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
1781			arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
1782			zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
1783			actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
1784			arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
1785			nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
1786			actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
1787	1.06652	5386.48	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	5744.78
1788	1.06651	5386.49	arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511]	5744.76
1789	1.06637	5839.72	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]	6227.33
1790			kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]
1791			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			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			cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
1794	1.06634	5948.26	epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964]	6342.84
1795	1.0663	5501.3	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]	5866.02
1796	1.06605	5387.64	tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7]	5743.5
1797		5096.02	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640]	5432.63
1798	1.06591	3618.02	60s ribosomal protein l32. [swissprot;acc:p02433]	3394.29
1799	1.0659	5456.57	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770]	5816.14
1800	1.06587	5424.3	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10]	5781.58
1801	1.06584	5881.33	epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333]	6268.57
1802	1.06571	4980.54	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	5307.81
1803			dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
1804			stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
1805			stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
1806	1.06568	4783.49	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	5097.66
1807	1.06542	6399.54	endothelial-derived gene 1. [refseq;acc:nm_025205]	6818.17
1808	1.06539	4941.92	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	5265.09
1809	1.06535	5816.12	epsin 3. [refseq;acc:nm_017957]	6196.21
1810	1.06532	6520.83	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	6946.75
1811	1.06494	7659.42	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]	8156.79
1812	1.06482	5514.19	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	5871.64
1813	1.06464	5866.19	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	6245.4
1814	1.06463	5733.71	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	6104.26
1815	1.06455	6104.77	junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624]	6498.84
1816	1.06454	5633.44	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122]	5997
1817			solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7]

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.