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

Results: HTML CSV LaTeX

Showing element 1463 to 1512 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
183	nuclear protein ukp68. [refseq;acc:nm_024824]	Measured	Subtracted	4241.57	5810.79	1569.22
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Rooted		47.6504	36.9304	10.72
184	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	Ranked		227.357	254.15	26.793
	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Rooted	Divided	153.602	133.195	1.15321
	ns1-associated protein 1. [refseq;acc:nm_006372]	Measured		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
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]		Divided	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
185	adiponectin receptor 2. [refseq;acc:nm_024551]	Ranked	Divided	281.582	246.371	1.14292
	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]		Subtracted	227.357	254.15	26.793
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Squared	Divided	41502.9	30836.8	1.34589
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]		Subtracted	70830.5	56822	14008.5
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Measured	Divided	4069.83	5252.17	1.29051
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Rooted		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
186	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	Squared		70830.5	56822	14008.5
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Measured	Divided	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
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Squared		41502.9	30836.8	1.34589
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Ranked	Subtracted	227.357	254.15	26.793
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Rooted	Divided	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
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted	Divided	153.548	133.153	1.15317
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Squared		41502.9	30836.8	1.34589
	mosaic protein lgn. [swissprot;acc:p81274]	Rooted	Subtracted	47.6504	36.9304	10.72
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Measured		4366.44	5899.76	1533.32
		Ranked	Divided	226.582	198.444	1.14179
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Measured		4569.48	5885.79	1.28807
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Ranked	Subtracted	227.357	254.15	26.793
188	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Squared	Divided	41502.9	30836.8	1.34589
	paraspeckle protein 1. [refseq;acc:nm_018282]		Subtracted	71360.3	57385.8	13974.5
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Measured		4366.44	5899.76	1533.32
		Ranked	Divided	226.582	198.444	1.14179
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Rooted	Subtracted	47.6504	36.9304	10.72
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Measured	Divided	4571.89	5864.86	1.28281
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Rooted		46.0352	53.0192	1.15171
189	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Ranked	Subtracted	241.373	267.352	25.979
	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]	Rooted		47.6504	36.9304	10.72
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Squared	Divided	41502.9	30836.8	1.34589
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Measured		4571.89	5864.86	1.28281
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]		Subtracted	4366.44	5899.76	1533.32
		Ranked	Divided	226.582	198.444	1.14179
	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	Subtracted	70694.1	56989.9	13704.2
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Rooted	Divided	46.0352	53.0192	1.15171

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.