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	green	red	network_comparison

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Showing element 483 to 532 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	green	red	network_comparison
242	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Subtracted	265.959	241.892	24.067
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Divided	254.15	227.357	1.11785
243	60s ribosomal protein l23a. [swissprot;acc:p29316]	Subtracted	265.945	241.884	24.061
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Divided	254.15	227.357	1.11785
244	60s ribosomal protein l5. [swissprot;acc:p46777]	Subtracted	265.924	241.899	24.025
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Divided	254.15	227.357	1.11785
245	60s ribosomal protein l19. [swissprot;acc:p14118]	Subtracted	264.729	240.73	23.999
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	202.333	226.109	1.11751
246	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Subtracted	267.528	243.583	23.945
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Divided	212.363	237.312	1.11748
247	60s ribosomal protein l12. [swissprot;acc:p30050]	Subtracted	267.527	243.583	23.944
	rna-binding protein. [refseq;acc:nm_019027]	Divided	212.41	237.302	1.11719
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Subtracted	267.527	243.583	23.944
249	ns1-associated protein 1. [refseq;acc:nm_006372]	Divided	212.41	237.302	1.11719
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Subtracted	202.333	226.109	23.776
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Divided	212.41	237.302	1.11719
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted	186.95	210.693	23.743
251	40s ribosomal protein s20. [swissprot;acc:p17075]		267.21	243.5	23.71
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Divided	166.661	186.172	1.11707
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		212.457	237.292	1.11689
	mad protein (max dimerizer). [swissprot;acc:q05195]	Subtracted	204.333	228	23.667
253		Divided			1.11583
	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	Subtracted	228.037	251.679	23.642
254	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		204.357	227.999
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Divided	179.88	200.691	1.11569
255	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted	204.366	227.999	23.633
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided	179.88	200.691	1.11569
256	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Subtracted	204.37	227.999	23.629
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided	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]		179.88	200.691
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Subtracted	265.697	242.14	23.557
258	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Divided	204.366	227.999	1.11564
259	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Subtracted	265.696	242.14	23.556
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Divided	204.37	227.999	1.11562
260	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]		196.978	219.421	1.11394
	surfeit locus protein 5. [swissprot;acc:q15528]	Subtracted	265.696	242.14	23.556
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Divided	196.978	219.421	1.11394
	zinc finger protein 291. [swissprot;acc:q9by12]	Subtracted	265.696	242.14	23.556
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Divided	196.978	219.421	1.11394
	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	Subtracted	265.696	242.14	23.556
263	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Divided	196.978	219.421	1.11394
	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	Subtracted	265.696	242.14	23.556
264	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]		266.796	243.24
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Divided	196.978	219.421	1.11394
265	60s ribosomal protein l9. [swissprot;acc:p32969]	Subtracted	263.798	240.243	23.555
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Divided	202.459	225.217	1.11241
266	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Subtracted	266.662	243.12	23.542
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Divided	267.88	241.07	1.11121

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.