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

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Showing element 551 to 600 of 29840 in total

Interaction Map  : High confidence

Rank	Network Comparison Type	description	Value Type	Filtered	green	network_comparison	red
35	Divided	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	0	4871.6	1.5182	3208.8
		nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]		1	204.309	1.27519	260.532
	Subtracted	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Rooted		122.878	17.63	140.508
		bystin. [swissprot;acc:q13895]	Squared	0	32857.7	6288	26569.7
		filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Measured		898	705	1603
		guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Ranked	1	335.359	67.723	267.636
		importin 9. [refseq;acc:nm_018085]		0	8691.76	4600.44	13292.2
		melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured	1	18263	5430.7	23693.7
		mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared		192141	85915	106226
		serpin b12. [swissprot;acc:q96p63]	Rooted	0	1.18697	9.10583	10.2928
36	Divided	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]			2.18581	1.96964	4.30525
		ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Ranked	1	204.309	1.27519	260.532
		cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Squared	0	8.01325	10.5625	84.64
		guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Ranked		14964	1.4984	22422
		guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Measured	1	907.741	2.02344	1836.76
			Rooted		24.369	1.65294	40.2805
		heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Measured	0	56	2.80357	157
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Squared	1	192141	1.80879	106226
	Subtracted	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]			146079	81081	227160
		huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]		0	369010	5957	363053
		hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Rooted		1.2188	9.0897	10.3085
		melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured	1	18263	5430.7	23693.7
		nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked	0	8691.76	4600.44	13292.2
		oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Measured		925.298	660.772	1586.07
		protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	1	254.434	66.493	320.927
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Rooted		43.1914	17.1626	26.0288
37	Divided	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	0	934.348	2.79409	334.401
			Squared		1034.13	10.2338	101.05
		dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Ranked		2582	1.49458	3859
		guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Measured	1	907.763	2.02339	1836.76
			Rooted		24.3691	1.65293	40.2805
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Squared		192141	1.80879	106226
		protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Ranked		253	1.27273	322
		small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Rooted	0	9.39626	1.94348	4.83477
	Subtracted	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Squared		38271.3	5857.6	32413.7
		dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Ranked		7533.33	4594.97	12128.3
		guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]		1	333.165	66.449	266.716
		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured		18263	5430.7	23693.7
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Rooted		43.1914	17.1626	26.0288
		nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]		0	25.3969	9.0874	16.3095
		trs85 homolog. [swissprot;acc:q9y2l5]	Squared	1	146079	81081	227160
		wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Measured	0	4550.64	652.25	5202.89
38	Divided	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Ranked		10771	1.48976	7230
		glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Squared		0.52284	9.25713	4.84
		guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Measured	1	907.774	2.02337	1836.76
			Rooted		24.3692	1.65292	40.2804
		microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Ranked		253	1.27273	322
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Squared		192141	1.80879	106226
		spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Rooted	0	6.97663	1.92709	3.62029
		zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Measured		120.429	2.65727	320.012

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.