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

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Showing element 218 to 267 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	green	red	network_comparison
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	126	112	1.125
219	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
220	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]
221	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
222	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]
223	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
224	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	165.623	185.969	1.12285
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	201.769	226.471	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	269.238	239.991	1.12187
227	thrombospondin 3 precursor. [swissprot;acc:p49746]	269.234	239.99	1.12186
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	202.088	226.411	1.12036
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	202.094	226.401	1.12028
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	267.915	239.35	1.11934
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	267.881	239.336	1.11927
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	267.879		1.11926
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	267.842	239.32	1.11918
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	256.835	287.41	1.11905
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	254.15	227.357	1.11785
236	pp3111 protein. [refseq;acc:nm_022156]
237	syntaxin 18. [swissprot;acc:q9p2w9]
238	rd protein. [swissprot;acc:p18615]
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]
242	j domain containing protein 1. [swissprot;acc:q9ukb3]
243	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]
244	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
245	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	202.333	226.109	1.11751
246	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	212.363	237.312	1.11748
247	rna-binding protein. [refseq;acc:nm_019027]	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]
249	ns1-associated protein 1. [refseq;acc:nm_006372]
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
251	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	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
253	mad protein (max dimerizer). [swissprot;acc:q05195]	204.333	228	1.11583
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	179.88	200.691	1.11569
255	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]
256	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	204.357	227.999
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
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	204.366	227.999	1.11564
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	204.37		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
261	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]
262	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
263	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
264	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]
265	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	202.459	225.217	1.11241
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	267.88	241.07	1.11121
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]

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.