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

Results: HTML CSV LaTeX

Showing element 1775 to 1824 of 3228 in total

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

Rank	description	red	green	network_comparison
1775	zinc finger protein 258. [refseq;acc:nm_145310]	5386.37	5744.89	1.06656
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	interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894]	5386.48	5744.78	1.06652
1788	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	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	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	epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964]	5948.26	6342.84	1.06634
1795	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	tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7]	5387.64	5743.5	1.06605
1797	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640]	5096.02	5432.63
1798	60s ribosomal protein l32. [swissprot;acc:p02433]	3618.02	3394.29	1.06591
1799	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	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9ui10]	5424.3	5781.58	1.06587
1801	epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333]	5881.33	6268.57	1.06584
1802	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818]	4980.54	5307.81	1.06571
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	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	endothelial-derived gene 1. [refseq;acc:nm_025205]	6399.54	6818.17	1.06542
1808	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046]	4941.92	5265.09	1.06539
1809	epsin 3. [refseq;acc:nm_017957]	5816.12	6196.21	1.06535
1810	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	6520.83	6946.75	1.06532
1811	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	hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	5514.19	5871.64	1.06482
1813	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]	5866.19	6245.4	1.06464
1814	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]	5733.71	6104.26	1.06463
1815	junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624]	6104.77	6498.84	1.06455
1816	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]	5633.44	5997	1.06454
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]
1818	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]
1819	adp-ribosylation factor 4. [swissprot;acc:p18085]
1820	fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]
1821	shc transforming protein. [swissprot;acc:p29353]
1822	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]
1823	neuronal shc. [refseq;acc:nm_016848]
1824	adp-ribosylation factor 1. [swissprot;acc:p32889]

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.