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	Value Type	description	Filtered	Network Comparison Type	Interaction Map	green	network_comparison	red

Results: HTML CSV LaTeX

Showing element 501 to 550 of 8289 in total

Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided

Rank	description	Interaction Map	green	network_comparison	red
251	nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505]	Low confidence	201.035	1.04666	210.415
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	High confidence	166.661	1.11707	186.172
252	cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839]	Low confidence	201.035	1.04665	210.414
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	High confidence	212.457	1.11689	237.292
253	mad protein (max dimerizer). [swissprot;acc:q05195]		204.333	1.11583	228
	nadph oxidase 4. [refseq;acc:nm_016931]	Low confidence	201.035	1.04665	210.413
254	nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718]				210.414
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	High confidence	179.88	1.11569	200.691
255	nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8]	Low confidence	201.035	1.04665	210.413
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	High confidence	179.88	1.11569	200.691
256	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		204.357		227.999
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Low confidence	190.521	1.04648	199.376
257	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]	High confidence	179.88	1.11569	200.691
	tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753]	Low confidence	192.404	1.04632	201.316
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	High confidence	204.366	1.11564	227.999
	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]	Low confidence	192.427	1.04613	201.304
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	High confidence	204.37	1.11562	227.999
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Low confidence	202.482	1.04599	211.794
260	ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527]		207.34	1.04589	216.855
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	High confidence	196.978	1.11394	219.421
261	ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560]	Low confidence	207.333	1.04588	216.845
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	High confidence	196.978	1.11394	219.421
262	breast cancer antigen ny-br-1. [refseq;acc:nm_052997]	Low confidence	207.332	1.04587	216.842
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	High confidence	196.978	1.11394	219.421
263	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
	sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581]	Low confidence	207.063	1.0458	216.546
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	High confidence	196.978	1.11394	219.421
	senescence downregulated leo1-like. [refseq;acc:nm_138792]	Low confidence	207.063	1.0458	216.546
265	solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591]
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	High confidence	202.459	1.11241	225.217
266	calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705]	Low confidence	205.509	1.04563	214.887
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	High confidence	267.88	1.11121	241.07
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
	tensin. [refseq;acc:nm_022648]	Low confidence	205.872	1.04559	215.258
268	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	High confidence	244.167	1.10996	271.016
	sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908]	Low confidence	199.455	1.04519	208.469
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	High confidence	267.352	1.10763	241.373
	sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610]	Low confidence	199.44	1.04511	208.436
270	fad synthetase. [refseq;acc:nm_025207]	High confidence	267.352	1.10763	241.373
	ring finger protein 10. [refseq;acc:nm_014868]	Low confidence	199.44	1.04511	208.437
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	High confidence	267.352	1.10763	241.373
	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]	Low confidence	192.595	1.04478	201.219
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	High confidence	267.352	1.10763	241.373
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Low confidence	208.421	1.04447	217.69
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]	High confidence	267.352	1.10763	241.373
	parafibromin. [refseq;acc:nm_024529]	Low confidence	204.916	1.0444	214.015
274	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]		200.653	1.04425	209.532
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	High confidence	267.352	1.10763	241.373
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Low confidence	191.203	1.04423	199.66

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.