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 2930 to 2979 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
184	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	Ranked	Subtracted	0	3284	4554.5	1270.5
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Measured			736.737	561.038	175.699
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]		Divided		375.07	306.727	1.22281
	calcyphosine. [swissprot;acc:q13938]	Rooted			18.8902	21.6141	1.1442
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]			1	153.602	133.195	1.15321
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]		Subtracted	0	23.8722	20.9333	2.9389
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Squared			3679.97	3222.25	457.72
	ns1-associated protein 1. [refseq;acc:nm_006372]	Measured	Divided	1	4069.83	5252.17	1.29051
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Ranked			274.027	237.79	1.15239
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Rooted	Subtracted		47.6504	36.9304	10.72
	pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498]	Squared			48127.9	62245.6	14117.7
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Ranked	Divided	0	6279.56	5569.42	1.12751
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Squared		1	72886.3	98544.5	1.35203
	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	Measured	Subtracted		10804.7	12363.6	1558.9
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Squared	Divided	0	4.23965	2.86829	1.47811
185	adiponectin receptor 2. [refseq;acc:nm_024551]	Ranked		1	281.582	246.371	1.14292
	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Squared		0	0.125207	0.0854438	1.46537
	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Ranked	Subtracted	1	227.357	254.15	26.793
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Measured	Divided	0	375.322	306.933	1.22281
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Squared		1	41502.9	30836.8	1.34589
	cab2. [refseq;acc:nm_033419]	Measured	Subtracted	0	0	174	174
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Rooted	Divided		30.6682	26.8335	1.14291
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared	Subtracted	1	70830.5	56822	14008.5
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Measured	Divided		4069.83	5252.17	1.29051
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Rooted	Subtracted	0	23.8722	20.9336	2.9386
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]		Divided	1	153.578	133.176	1.1532
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]		Subtracted		47.6504	36.9304	10.72
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	Measured			4599.26	3058.57	1540.69
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Squared		0	3679.95	3222.24	457.71
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	Ranked			3284	4554.5	1270.5
	zinc finger protein 277. [swissprot;acc:q9nrm2]		Divided		6279.56	5569.42	1.12751
186	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]				11935.1	10592.8	1.12672
	60s ribosomal protein l15. [swissprot;acc:p39030]	Rooted			19.482	17.0546	1.14233
	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	Squared	Subtracted	1	70830.5	56822	14008.5
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Ranked		0	12677.7	13941.7	1264
	espin. [refseq;acc:nm_031475]	Squared			3679.78	3222.11	457.67
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Measured			633.85	460.2	173.65
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		Divided	1	4071.1	5251.75	1.29001
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]		Subtracted		4366.44	5899.76	1533.32
		Ranked	Divided		226.582	198.444	1.14179
	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	Measured		0	470.251	384.733	1.22228
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Squared		1	41502.9	30836.8	1.34589
	huntingtin interacting protein c. [refseq;acc:nm_012272]			0	5086.87	3492.66	1.45645
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Ranked	Subtracted	1	227.357	254.15	26.793
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Rooted		0	23.8722	20.9336	2.9386
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		Divided	1	153.578	133.176	1.1532
	transcription factor lbx1. [swissprot;acc:p52954]		Subtracted		47.6504	36.9304	10.72
187	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]	Squared			71383	57399.3	13983.7
	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Ranked	Divided	0	9955.22	11213.7	1.12641
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted		1	153.548	133.153	1.15317

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.