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 510 to 559 of 3730 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
255	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	0	10551.6	11573.5	1.09685
256	espin. [refseq;acc:nm_031475]			11573.4	1.09684
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	1	227.999	204.357	1.11569
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]		200.691	179.88
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	0	10552.2	11566.4	1.09611
258	40s ribosomal protein s28. [swissprot;acc:p25112]		12967.1	14193.6	1.09459
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	1	227.999	204.366	1.11564
259	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	0	10438.3	9549.77	1.09304
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	1	227.999	204.37	1.11562
260	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	0	12447.6	11392.6	1.0926
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	1	219.421	196.978	1.11394
261	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	0	12448.9	11393.9	1.09259
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	1	219.421	196.978	1.11394
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	0	3464	3778	1.09065
263	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		13573.3	14801.2	1.09046
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	1	219.421	196.978	1.11394
264	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	0	10037.1	10935.1	1.08947
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	1	219.421	196.978	1.11394
265	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	0	13653.8	14874	1.08937
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	1	225.217	202.459	1.11241
266	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	0	13483.3	14685.4	1.08915
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	1	241.07	267.88	1.11121
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	0	8054.34	8772.02	1.0891
268	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	1	271.016	244.167	1.10996
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	0	14257.4	13134.5	1.08549
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]	1	241.373	267.352	1.10763
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	0	12463.5	11482.6	1.08542
270	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]		10735.1	9891.37	1.0853
	fad synthetase. [refseq;acc:nm_025207]	1	241.373	267.352	1.10763
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]
	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	0	10735.1	9891.37	1.0853
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	1	241.373	267.352	1.10763
	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	0	7163.55	7759.61	1.08321
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]	1	241.373	267.352	1.10763
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	0	12748.1	11770.9	1.08302
274	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]		10432.4	11298.4	1.08301
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	1	241.373	267.352	1.10763
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]
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	0	10783	11674.1	1.08264
276	60s ribosomal protein l32. [swissprot;acc:p02433]	1	241.13	266.969	1.10716
	60s ribosomal protein l9. [swissprot;acc:p32969]	0	10741.6	9922.33	1.08257
277	40s ribosomal protein s29. [swissprot;acc:p30054]	1	241.849	267.642	1.10665
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	0	11096.8	10251.6	1.08245
278	40s ribosomal protein s11. [swissprot;acc:p04643]	1	241.399	267.088	1.10642
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	0	11644	10763.4	1.08181
279	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]		10614.2	9812.39	1.08171
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	1	252.644	228.42	1.10605
280	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	0	10620.1	11471.2	1.08014

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.