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 2980 to 3029 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
187	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Measured	Subtracted	0	210.767	384.407	173.64
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Squared	Divided	1	41502.9	30836.8	1.34589
	importin 9. [refseq;acc:nm_018085]	Measured		0	1143.55	1397.66	1.22221
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Rooted	Subtracted		23.8722	20.9337	2.9385
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Squared			3665.1	3211.04	454.06
	mosaic protein lgn. [swissprot;acc:p81274]	Rooted		1	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
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]		Subtracted	0	14003.7	12743.3	1260.4
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Measured	Divided	1	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
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Squared	Divided	0	8660.1	5963.73	1.45213
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Rooted			32.4121	28.377	1.1422
188	60s ribosomal protein l15. [swissprot;acc:p39030]	Ranked			11745.2	13203.1	1.12413
	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Squared	Subtracted		7496.94	7944.03	447.09
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Ranked		1	227.357	254.15	26.793
	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
	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Measured		0	1143.55	1397.66	1.22221
	paraspeckle protein 1. [refseq;acc:nm_018282]	Squared	Subtracted	1	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
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Measured		0	1410.81	1582.65	171.84
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]		Divided	1	4571.89	5864.86	1.28281
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Rooted	Subtracted	0	23.8722	20.9337	2.9385
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Ranked			8409.21	9668.79	1259.58
	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	Divided	1	46.0352	53.0192	1.15171
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Squared		0	157.095	228.024	1.4515
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Rooted			32.4121	28.377	1.1422
189	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Ranked	Subtracted		9955.22	11213.7	1258.48
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]			1	241.373	267.352	25.979
	espin. [refseq;acc:nm_031475]	Rooted		0	23.8722	20.934	2.9382
	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]			1	47.6504	36.9304	10.72
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Measured		0	6830.67	7000.85	170.18
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Squared	Divided	1	41502.9	30836.8	1.34589
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]			0	232467	160184	1.45125
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Measured		1	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
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Measured		0	1249.24	1023.76	1.22025
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Ranked			10634.4	9465	1.12355
	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	1	70694.1	56989.9	13704.2
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]			0	1110.11	669.13	440.98
		Rooted	Divided	1	46.0352	53.0192	1.15171
	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]			0	32.4121	28.377	1.1422
190	adp-ribosylation factor 3. [swissprot;acc:p16587]	Measured	Subtracted		300.697	469.346	168.649
	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Squared			439.709	0.52284	439.186
	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]		Divided	1	71389.9	96037.6	1.34525
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Measured			4571.89	5864.86	1.28281
	fad synthetase. [refseq;acc:nm_025207]	Ranked	Subtracted		241.373	267.352	25.979

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.