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	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison	Filtered

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Showing element 451 to 500 of 3730 in total

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

Rank	description	red	green	network_comparison	Filtered
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	239.991	269.238	1.12187	1
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	15395.7	16992.9	1.10374	0
227	thrombospondin 3 precursor. [swissprot;acc:p49746]	239.99	269.234	1.12186	1
	tigger transposable element derived 6. [refseq;acc:nm_030953]	12360	11200.2	1.10355	0
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	1
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	10303.5	11370.4	1.10355	0
229	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	226.401	202.094	1.12028	1
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	10899.4	9878.1	1.10339	0
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	239.35	267.915	1.11934	1
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	12364.7	11207.7	1.10323	0
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	239.336	267.881	1.11927	1
	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	12364.8	11207.9	1.10322	0
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]	239.336	267.879	1.11926	1
233	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	9586.97	10560	1.1015	0
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	239.32	267.842	1.11918	1
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]	16614	18296	1.10124	0
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]	227.357	254.15	1.11785	1
236	pp3111 protein. [refseq;acc:nm_022156]
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	15245.4	16788.5	1.10122	0
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]	227.357	254.15	1.11785	1
238	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	12677.7	13941.7	1.0997	0
	rd protein. [swissprot;acc:p18615]	227.357	254.15	1.11785	1
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	8907.41	9795.36	1.09969	0
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	227.357	254.15	1.11785	1
	methyltransferase like 2. [refseq;acc:nm_018396]	17946	16326	1.09923	0
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	227.357	254.15	1.11785	1
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	14003.7	12743.3	1.09891	0
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]	227.357	254.15	1.11785	1
243	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	1251	1373	1.09752	0
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	227.357	254.15	1.11785	1
244	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
	keratin associated protein 9.2. [refseq;acc:nm_031961]	10551.1	11579.9	1.09751	0
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]	226.109	202.333	1.11751	1
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]	10551.6	11573.7	1.09687	0
247	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
	rna-binding protein. [refseq;acc:nm_019027]	237.302	212.41	1.11719	1
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]	10551.6	11573.7	1.09687	0
249	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
	ns1-associated protein 1. [refseq;acc:nm_006372]	237.302	212.41	1.11719	1
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	10551.6	11573.7	1.09687	0

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.