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 210 to 259 of 3228 in total

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

Rank	description	red	green	network_comparison
210	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	285.684	252.234	1.13261
211	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
212	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
213	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	210.693	186.95	1.127
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	191.644	170.192	1.12605
215	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	112	126	1.125
216	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
217	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
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]	185.969	165.623	1.12285
225	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	239.991	269.238	1.12187
227	thrombospondin 3 precursor. [swissprot;acc:p49746]	239.99	269.234	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]	226.411	202.088	1.12036
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	226.401	202.094	1.12028
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	239.35	267.915	1.11934
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	239.336	267.881	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]	239.32	267.842	1.11918
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	287.41	256.835	1.11905
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	227.357	254.15	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]	226.109	202.333	1.11751
246	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	237.312	212.363	1.11748
247	rna-binding protein. [refseq;acc:nm_019027]	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]
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]	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
253	mad protein (max dimerizer). [swissprot;acc:q05195]	228	204.333	1.11583
254	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	200.691	179.88	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]	227.999	204.357
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
258	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	227.999	204.366	1.11564
259	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		204.37	1.11562

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.