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

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Showing element 451 to 500 of 3730 in total

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

Rank	description	Filtered	red	green	network_comparison
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	1	239.991	269.238	1.12187
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	0	15395.7	16992.9	1.10374
227	thrombospondin 3 precursor. [swissprot;acc:p49746]	1	239.99	269.234	1.12186
	tigger transposable element derived 6. [refseq;acc:nm_030953]	0	12360	11200.2	1.10355
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]	1	226.411	202.088	1.12036
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	0	10303.5	11370.4	1.10355
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	1	226.401	202.094	1.12028
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	0	10899.4	9878.1	1.10339
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	1	239.35	267.915	1.11934
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	0	12364.7	11207.7	1.10323
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	1	239.336	267.881	1.11927
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	0	12364.8	11207.9	1.10322
232	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]		12394.7	11240.2	1.10271
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	1	239.336	267.879	1.11926
233	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	0	9586.97	10560	1.1015
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	1	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
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	0	16614	18296	1.10124
235	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]		14554.5	16027.9	1.10123
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	1	227.357	254.15	1.11785
236	pp3111 protein. [refseq;acc:nm_022156]
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	0	15245.4	16788.5	1.10122
237	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]		9984	9067	1.10114
	syntaxin 18. [swissprot;acc:q9p2w9]	1	227.357	254.15	1.11785
238	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	0	12677.7	13941.7	1.0997
	rd protein. [swissprot;acc:p18615]	1	227.357	254.15	1.11785
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	0	8907.41	9795.36	1.09969
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	1	227.357	254.15	1.11785
	methyltransferase like 2. [refseq;acc:nm_018396]	0	17946	16326	1.09923
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	1	227.357	254.15	1.11785
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	0	14003.7	12743.3	1.09891
242	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]		15260.6	13895.8	1.09822
	j domain containing protein 1. [swissprot;acc:q9ukb3]	1	227.357	254.15	1.11785
243	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	0	1251	1373	1.09752
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	1	227.357	254.15	1.11785
244	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
	keratin associated protein 9.2. [refseq;acc:nm_031961]	0	10551.1	11579.9	1.09751
245	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]		11867.6	13019	1.09702
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	1	226.109	202.333	1.11751
246	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]		237.312	212.363	1.11748
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	0	10551.6	11573.7	1.09687
247	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
	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]
	keratin associated protein 1.5. [refseq;acc:nm_031957]	0	10551.6	11573.7	1.09687
249	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
	ns1-associated protein 1. [refseq;acc:nm_006372]	1	237.302	212.41	1.11719
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	0	10551.6	11573.7	1.09687

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.