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 975 to 1024 of 7460 in total

Value Type  : Ranked
Interaction Map  : High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison
244	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Subtracted	0	10551.6	11573.5	1021.9
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Divided		10551.1	11579.9	1.09751
245	60s ribosomal protein l19. [swissprot;acc:p14118]	Subtracted	1	240.73	264.729	23.999
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Divided	0	11867.6	13019	1.09702
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Subtracted		10551.6	11573.5	1021.9
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	1	226.109	202.333	1.11751
246	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Subtracted		243.583	267.528	23.945
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Divided		237.312	212.363	1.11748
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]		0	10551.6	11573.7	1.09687
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Subtracted			11573.5	1021.9
247	60s ribosomal protein l12. [swissprot;acc:p30050]		1	243.583	267.527	23.944
	espin. [refseq;acc:nm_031475]		0	10551.6	11573.4	1021.8
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Divided			11573.7	1.09687
	rna-binding protein. [refseq;acc:nm_019027]		1	237.302	212.41	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		243.583	267.527	23.944
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Divided	0	10551.6	11573.7	1.09687
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Subtracted		10899.4	9878.1	1021.3
249	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]			10552.2	11566.4	1014.2
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Divided		10551.6	11573.7	1.09687
	ns1-associated protein 1. [refseq;acc:nm_006372]		1	237.302	212.41	1.11719
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Subtracted		226.109	202.333	23.776
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Divided		237.302	212.41	1.11719
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]		0	10551.6	11573.7	1.09687
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted	1	210.693	186.95	23.743
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]		0	12522.7	13514.5	991.8
251	40s ribosomal protein s20. [swissprot;acc:p17075]		1	243.5	267.21	23.71
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]		0	12463.5	11482.6	980.9
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]	Divided		10551.6	11573.6	1.09686
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]		1	186.172	166.661	1.11707
252	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]			237.292	212.457	1.11689
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]		0	10551.6	11573.5	1.09685
	mad protein (max dimerizer). [swissprot;acc:q05195]	Subtracted	1	228	204.333	23.667
	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	977.2
253	60s acidic ribosomal protein p1. [swissprot;acc:p05386]			9586.97	10560	973.03
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Divided		10551.6	11573.5	1.09685
	mad protein (max dimerizer). [swissprot;acc:q05195]		1	228	204.333	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		251.679	228.037	23.642
254	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Divided	0	10551.6	11573.5	1.09685
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Subtracted	1	227.999	204.357	23.642
	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]		0	17387.1	16427.3	959.8
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Divided	1	200.691	179.88	1.11569
255	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted		227.999	204.366	23.633
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided		200.691	179.88	1.11569
	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Subtracted	0	17387.1	16427.3	959.8
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Divided		10551.6	11573.5	1.09685
256	espin. [refseq;acc:nm_031475]				11573.4	1.09684
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Subtracted	1	227.999	204.37	23.629
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided			204.357	1.11569
	transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514]	Subtracted	0	13981.5	13025.1	956.4

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.