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

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Showing element 551 to 600 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
35	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Measured	Subtracted	0	1603	898	705
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Ranked		1	267.636	335.359	67.723
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Measured	Divided		1836.71	907.564	2.02378
		Rooted			40.2812	24.3679	1.65304
	importin 9. [refseq;acc:nm_018085]	Ranked	Subtracted	0	13292.2	8691.76	4600.44
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured		1	23693.7	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared			106226	192141	85915
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	Divided	0	3208.8	4871.6	1.5182
	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	260.532	204.309	1.27519
	serpin b12. [swissprot;acc:q96p63]	Rooted	Subtracted	0	10.2928	1.18697	9.10583
36	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]		Divided		4.30525	2.18581	1.96964
	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	260.532	204.309	1.27519
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Squared		0	84.64	8.01325	10.5625
	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]		Subtracted	1	227160	146079	81081
	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	Divided	0	22422	14964	1.4984
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Measured		1	1836.76	907.741	2.02344
		Rooted			40.2805	24.369	1.65294
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Measured		0	157	56	2.80357
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Squared	Subtracted		363053	369010	5957
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Rooted			10.3085	1.2188	9.0897
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured		1	23693.7	18263	5430.7
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Ranked		0	13292.2	8691.76	4600.44
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Measured			1586.07	925.298	660.772
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Squared	Divided	1	106226	192141	1.80879
	protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690]	Ranked	Subtracted		320.927	254.434	66.493
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Rooted			26.0288	43.1914	17.1626
37	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Measured	Divided	0	334.401	934.348	2.79409
		Squared			101.05	1034.13	10.2338
	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	Ranked			3859	2582	1.49458
	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Squared	Subtracted		32413.7	38271.3	5857.6
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Ranked			12128.3	7533.33	4594.97
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]			1	266.716	333.165	66.449
	guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488]	Measured	Divided		1836.76	907.763	2.02339
		Rooted			40.2805	24.3691	1.65293
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured	Subtracted		23693.7	18263	5430.7
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Rooted			26.0288	43.1914	17.1626
	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	16.3095	25.3969	9.0874
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Squared	Divided	1	106226	192141	1.80879
	protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256]	Ranked			322	253	1.27273
	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	4.83477	9.39626	1.94348
	trs85 homolog. [swissprot;acc:q9y2l5]	Squared	Subtracted	1	227160	146079	81081
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Measured		0	5202.89	4550.64	652.25
38	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Ranked	Divided		7230	10771	1.48976
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Measured	Subtracted		5497.01	6127.24	630.23
	ero1-like. [refseq;acc:nm_014584]	Rooted			9.05539	0	9.05539
	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]	Squared	Divided		4.84	0.52284	9.25713
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Ranked	Subtracted	1	266.933	333.281	66.348
	guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087]	Measured	Divided		1836.76	907.774	2.02337
		Rooted			40.2804	24.3692	1.65292
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured	Subtracted		23693.7	18263	5430.7

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.