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 1 to 32 of 32 in total

Rank  : 2

description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Measured	Subtracted	Low confidence	1	21185	28492	7307
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Ranked		High confidence	0	4294	15915	11621
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]	Squared		Low confidence	1	333556	475119	141563
cab2. [refseq;acc:nm_033419]	Measured	Divided	High confidence	0	0.00001	174	17400000
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802]			Low confidence	1	2399.5	543.5	4.4149
	Ranked	Subtracted			223	330	107
	Squared	Divided			1362.75	69.9153	19.4914
	Rooted				48.9847	23.3131	2.10117
		Subtracted					25.6716
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Measured		High confidence		41482.5	33356.5	8126
hbs1-like. [refseq;acc:nm_006620]	Ranked				215	322	107
histone h4. [swissprot;acc:p02304]	Squared			0	273623	345123	71500
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Measured	Divided	Low confidence		0.00001	89	8900000
	Rooted					9.43398	943398
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared					1.87479	187479
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured	Subtracted	High confidence		85	6410	6325
	Rooted				9.20014	60.0707	50.8706
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279]	Ranked	Divided	Low confidence	1	223	330	1.47982
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]			High confidence		15	28	1.86667
	Squared	Subtracted			407289	263351	143938
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Ranked	Divided	Low confidence	0	8906	21883	2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]			High confidence		5865	14977	2.55362
	Rooted	Subtracted	Low confidence		29.3087	7.61577	21.6929
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Ranked				9607	20617	11010
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured				23818.1	19621.3	4196.8
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	Divided	High confidence		5.61325	0.00001	561325
	Rooted				12.4097		1240970
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured			1	450.5	2394.5	5.31521
	Squared				48.0356	1357.07	28.2513
	Rooted				21.225	48.9336	2.30547
		Subtracted					27.7086
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Squared		Low confidence	0	414704	386144	28560

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.