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

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Showing element 451 to 500 of 7460 in total

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

Rank	green	description	Filtered	network_comparison	red
226	269.238	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	1	1.12187	239.991
	16992.9	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	0	1.10374	15395.7
227	269.234	thrombospondin 3 precursor. [swissprot;acc:p49746]	1	1.12186	239.99
	11200.2	tigger transposable element derived 6. [refseq;acc:nm_030953]	0	1.10355	12360
228	202.088	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	1.12036	226.411
	11370.4	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	0	1.10355	10303.5
229	202.094	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	1	1.12028	226.401
	9878.1	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	0	1.10339	10899.4
230	267.915	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	1	1.11934	239.35
	11207.7	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	0	1.10323	12364.7
231	267.881	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	1	1.11927	239.336
	11207.9	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	0	1.10322	12364.8
232	267.879	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	1	1.11926	239.336
	11240.2	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	0	1.10271	12394.7
233	267.842	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	1	1.11918	239.32
	10560	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	0	1.1015	9586.97
234	256.835	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	1	1.11905	287.41
	18296	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	0	1.10124	16614
235	254.15	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	1	1.11785	227.357
	16027.9	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	0	1.10123	14554.5
236	254.15	pp3111 protein. [refseq;acc:nm_022156]	1	1.11785	227.357
	16788.5	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	0	1.10122	15245.4
237	254.15	syntaxin 18. [swissprot;acc:q9p2w9]	1	1.11785	227.357
	9067	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]	0	1.10114	9984
238	254.15	rd protein. [swissprot;acc:p18615]	1	1.11785	227.357
	13941.7	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	0	1.0997	12677.7
239	254.15	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	1	1.11785	227.357
	9795.36	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	0	1.09969	8907.41
240	254.15	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	1	1.11785	227.357
	16326	methyltransferase like 2. [refseq;acc:nm_018396]	0	1.09923	17946
241	254.15	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	1	1.11785	227.357
	12743.3	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	0	1.09891	14003.7
242	254.15	j domain containing protein 1. [swissprot;acc:q9ukb3]	1	1.11785	227.357
	13895.8	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	0	1.09822	15260.6
243	254.15	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	1	1.11785	227.357
	1373	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	0	1.09752	1251
244	254.15	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	1	1.11785	227.357
	11579.9	keratin associated protein 9.2. [refseq;acc:nm_031961]	0	1.09751	10551.1
245	202.333	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	1	1.11751	226.109
	13019	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	0	1.09702	11867.6
246	212.363	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	1	1.11748	237.312
	11573.7	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	0	1.09687	10551.6
247	212.41	rna-binding protein. [refseq;acc:nm_019027]	1	1.11719	237.302
	11573.7	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	0	1.09687	10551.6
248	212.41	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	1	1.11719	237.302
	11573.7	keratin associated protein 1.5. [refseq;acc:nm_031957]	0	1.09687	10551.6
249	212.41	ns1-associated protein 1. [refseq;acc:nm_006372]	1	1.11719	237.302
	11573.7	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	0	1.09687	10551.6
250	212.41	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	1	1.11719	237.302
	11573.7	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	0	1.09687	10551.6

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.