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 268 to 317 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
34	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured	Divided	1836.71	907.546	2.02382
		Rooted		40.2812	24.3678	1.65305
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Measured	Subtracted	23693.7	18263	5430.7
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Squared		106226	192141	85915
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Ranked	Divided	189.07	242.453	1.28235
35	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Squared		106226	192141	1.80879
	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Rooted	Subtracted	140.508	122.878	17.63
	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775]	Ranked		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
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured	Subtracted	23693.7	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared		106226	192141	85915
	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]	Ranked	Divided	260.532	204.309	1.27519
36	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]
	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]	Squared	Subtracted	227160	146079	81081
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Measured	Divided	1836.76	907.741	2.02344
		Rooted		40.2805	24.369	1.65294
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured	Subtracted	23693.7	18263	5430.7
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Squared	Divided	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	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	Ranked		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
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Squared	Divided	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
	trs85 homolog. [swissprot;acc:q9y2l5]	Squared	Subtracted	227160	146079	81081
38	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Ranked		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
	microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083]	Ranked	Divided	322	253	1.27273
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Squared		106226	192141	1.80879
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Rooted	Subtracted	26.0288	43.1914	17.1626
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Squared		226186	145568	80618
39	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]	Rooted		26.0288	43.1914	17.1626
	guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899]	Measured	Divided	1836.8	907.903	2.02312
		Rooted		40.28	24.37	1.65285
	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]	Ranked	Subtracted	268.565	334.483	65.918
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured		23693.7	18263	5430.7
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Squared	Divided	106226	192141	1.80879
	protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726]	Ranked		322	253	1.27273
40	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Squared	Subtracted	222655	143584	79071
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		Divided	144940	81169.7	1.78564
	deltex 2. [refseq;acc:nm_020892]	Ranked	Subtracted	333.144	267.393	65.751
	ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485]		Divided	322	253	1.27273
	guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898]	Measured		1836.81	907.978	2.02297

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.