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

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Showing element 401 to 450 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	green	network_comparison
aarf domain containing kinase 4. [refseq;acc:nm_024876]	1728	Subtracted	1	215.336	212.567	2.769
	1732	Divided				1.01303
abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	1912	Subtracted		218.43	216.279	2.151
	1935	Divided				1.00995
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759]	1837	Subtracted		217.077	214.702	2.375
	1845	Divided				1.01106
acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752]	2306			191.571	192.544	1.00508
	2338	Subtracted				0.973
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085]	2319	Divided		194.842	195.8	1.00492
	2344	Subtracted				0.958
acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	2315	Divided		194.825	195.787	1.00494
	2341	Subtracted				0.962
acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	2039	Divided		190.551	192.191	1.00861
	2085	Subtracted				1.64
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	1417			207.076	211.391	4.315
	1421	Divided				1.02084
acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	21		0	6313.38	10621.4	1.68236
	39	Subtracted				4308.02
	2101	Divided	1	211.71	213.27	1.00737
		Subtracted				1.56
actin binding lim protein 2. [refseq;acc:nm_032432]	625			229.072	216.576	12.496
	660	Divided				1.0577
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	382		0	10449	10061.8	1.03848
	390	Subtracted				387.2
	1529	Divided	1	216.762	213.031	1.01751
	1536	Subtracted				3.731
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	633			229.072	216.576	12.496
	668	Divided				1.0577
actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	2603	Subtracted		224.891	225.195	0.304
	2626	Divided				1.00135
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]	2608	Subtracted				0.304
	2631	Divided				1.00135
actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]	2611	Subtracted				0.304
	2634	Divided				1.00135
activated p21cdc42hs kinase. [refseq;acc:nm_005781]	2317	Subtracted		229.258	230.294	1.036
	2341	Divided				1.00452
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	1137	Subtracted		219.399	213.784	5.615
	1169	Divided				1.02626
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	1044	Subtracted		269.157	275.531	6.374
	1303	Divided				1.02368
activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	1288	Subtracted		223.884	228.795	4.911
	1366	Divided				1.02194
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [swissprot;acc:q04771]	3050			0.00001	0.00001	1
		Subtracted		0	0	0
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561]	2498	Divided		194.527	195.08	1.00284
	2509	Subtracted				0.553
acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	1412			206.102	210.42	4.318
	1413	Divided				1.02095
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	62	Subtracted	0	17410.5	14360	3050.5
	105	Divided				1.21243

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.