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

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Showing element 451 to 500 of 77072 in total

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green	Value Type	network_comparison	Interaction Map	red	Network Comparison Type	Rank	description
3.87298	Rooted	2.87298	High confidence	1	Subtracted	192	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]
		3.87298			Divided	23
3.99932	Squared	3.12701		0.872309	Subtracted	427	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]
		4.58475			Divided	51
4.11238		1.61589	Low confidence	2.49649	Subtracted	800	trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477]
		1.64726			Divided	142
4.17869		0.68559		3.4931	Subtracted	811	phenol-sulfating phenol sulfotransferase 1 (ec 2.8.2.1) (p-pst) (thermostable phenol sulfotransferase) (ts-pst) (hast1/hast2) (st1a3). [swissprot;acc:p50225]
		1.19627			Divided	280
4.1804		0.68915		3.49125	Subtracted	809	phenol-sulfating phenol sulfotransferase 2 (ec 2.8.2.1) (p-pst) (st1a2). [swissprot;acc:p50226]
						810	monoamine-sulfating phenol sulfotransferase (ec 2.8.2.1) (sulfotransferase, monoamine-preferring) (m-pst) (thermolabile phenol sulfotransferase) (tl-pst) (placental estrogen sulfotransferase) (catecholamine-sulfating phenol sulfotransferase) (hast3). [swissprot;acc:p50224]
		1.19739			Divided	276	phenol-sulfating phenol sulfotransferase 2 (ec 2.8.2.1) (p-pst) (st1a2). [swissprot;acc:p50226]
						277	monoamine-sulfating phenol sulfotransferase (ec 2.8.2.1) (sulfotransferase, monoamine-preferring) (m-pst) (thermolabile phenol sulfotransferase) (tl-pst) (placental estrogen sulfotransferase) (catecholamine-sulfating phenol sulfotransferase) (hast3). [swissprot;acc:p50224]
4.24264	Rooted	4.24264	High confidence	0	Subtracted	116	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]
		424264		0.00001	Divided	14
4.3589		0.43693		4.79583	Subtracted	445	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]
			Low confidence			722
		1.10024	High confidence		Divided	263
			Low confidence			359
		2.28266		9.94987		18	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]
		5.59097			Subtracted	50
4.57302	Squared	16.8159	High confidence	76.8994	Divided	32	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
						33	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
			Low confidence			21
		72.3264	High confidence		Subtracted	303	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
						304	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
			Low confidence			628
4.58258	Rooted	1.44749	High confidence	6.63325	Divided	61	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]
		2.05067			Subtracted	274
4.6274		1.1455		3.4819		352	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]
			Low confidence			544
		1.32899	High confidence		Divided	88
			Low confidence			93
4.74982	Squared	1.71779	High confidence	8.15919		146	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]
		3.40937			Subtracted	424
4.90793		1.68639		8.27669	Divided	149	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]
		2.0736		2.36686		105	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]
		2.54107			Subtracted	433
		3.36876		8.27669		425	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]
5.11062		4.17059	Low confidence	21.3143	Divided	60	fos39347_1. [sptrembl;acc:o75863]
		16.2037			Subtracted	736
5.12693	Rooted	3.47237	High confidence	17.8026	Divided	27	dystrophin. [swissprot;acc:p11532]
		12.6757			Subtracted	16
5.15101	Squared	4.12321	Low confidence	21.2387	Divided	62	dj254p11.1 (novel protein similar to rna polymerase ii elongation factor siii, subunit p15). [sptrembl;acc:q9h575]
		16.0877			Subtracted	738
5.24885		1.67729	High confidence	8.80383	Divided	152	40s ribosomal protein s26. [swissprot;acc:p02383]
		3.55498			Subtracted	423
5.33358		8.22384		43.8625	Divided	39	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]
		38.5289			Subtracted	343
5.38516	Rooted	1.28654	Low confidence	6.9282	Divided	102	abl-philin 2. [refseq;acc:nm_032327]
		1.54304			Subtracted	457

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.