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 5580 to 5629 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2790	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]	Subtracted	0	0	0
2791	cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2792	transcription factor maf (proto-oncogene c-maf). [swissprot;acc:o75444]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2793	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2794	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2795	nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2796	dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2797	sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2798	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2799	hmg2 like. [refseq;acc:nm_145205]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2800	mondoa. [refseq;acc:nm_014938]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2801	dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2802	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2803	nanos (fragment). [sptrembl;acc:q8wy41]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2804	barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2805	phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [refseq;acc:nm_018026]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2806	spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2807	ras-related protein rab-1b. [swissprot;acc:q9h0u4]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2808	dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2809	polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2810	udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2811	vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2812	mob-lak. [refseq;acc:nm_130807]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2813	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2814	spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2815	g protein-coupled receptor 66. [refseq;acc:nm_006056]	Divided	0.00001	0.00001	1

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.