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 5758 to 5807 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
360	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Squared	Divided	1	9814.47	7911.48	1.24054
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Measured	Subtracted		4590.18	5575.52	985.34
	vav-2 protein. [swissprot;acc:p52735]	Squared			31377.3	37670.1	6292.8
361	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Rooted	Divided		50.7801	45.9472	1.10518
	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]		Subtracted		46.8525	53.5324	6.6799
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Measured			6875.08	7858.38	983.3
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]		Divided		12787.6	10880.5	1.17528
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Rooted		0	27.5221	28.7585	1.04492
	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Ranked	Subtracted	1	232.431	252.238	19.807
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		Divided	0	16321	15577	1.04776
		Squared			0.545325	0.615621	1.12891
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured			48	51	1.0625
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Ranked		1	242.83	266.248	1.09644
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Squared	Subtracted	0	98.1677	70.141	28.0267
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Ranked			14223.9	14738.5	514.6
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Rooted			21.9882	20.9119	1.0763
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Measured			634.305	584.237	50.068
	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	Squared	Divided	1	70694.1	56989.9	1.24047
	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]		Subtracted		42363.8	36083.8	6280
362	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Rooted	Divided		50.7803	45.9477	1.10518
	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]			0	27.5242	28.7604	1.04491
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Ranked		1	231.492	211.136	1.09641
	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Rooted	Subtracted		46.8525	53.5316	6.6791
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Ranked		0	10540.6	10027.6	513
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	Divided	1	12786.6	10879.9	1.17525
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]		Subtracted	0	244	194	50
	germ cell-less. [refseq;acc:nm_022471]	Rooted			27.8491	26.7806	1.0685
	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Ranked		1	232.382	252.166	19.784
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]		Divided	0	16321	15577	1.04776
		Squared			0.545325	0.615621	1.12891
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured			48	51	1.0625
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Squared	Subtracted		98.1677	70.141	28.0267
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]			1	34071.5	40336.5	6265
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Measured			4981.52	5964.58	983.06
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Squared	Divided		57808.9	46630.3	1.23973
363	40s ribosomal protein s3a. [swissprot;acc:p49241]	Measured	Subtracted	0	2929.51	2879.55	49.96
	60s ribosomal protein l18a. [swissprot;acc:q02543]	Rooted	Divided		30.8547	32.2238	1.04437
	alpha-nac protein. [sptrembl;acc:q9h009]	Squared	Subtracted	1	34069.4	40333	6263.6
	block of proliferation 1. [swissprot;acc:q14137]	Rooted	Divided		49.4884	54.6735	1.10477
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Ranked	Subtracted	0	16680.7	17180.3	499.6
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Measured	Divided	1	12780.7	10876.4	1.17509
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]			0	48	51	1.0625
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Ranked			16321	15577	1.04776
		Squared			0.545325	0.615621	1.12891
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]		Subtracted		98.1677	70.141	28.0267
	scratch; scratch 1. [refseq;acc:nm_031309]	Rooted			21.5021	20.4389	1.0632
	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Ranked		1	233.539	253.197	19.658
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]		Divided		231.481	211.131	1.09639
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Measured	Subtracted		6856.71	7838.3	981.59
	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Squared	Divided		57579.2	46497.2	1.23834

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.