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	Interaction Map	Value Type	green	red	network_comparison	Filtered

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Showing element 451 to 500 of 3730 in total

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

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