Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 2377 to 2426 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1189	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [source:swissprot;acc:p19652]	Divided	209.649	204.406	1.02565	
1189	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]	Subtracted	219.354	224.7	5.346	
1190	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [source:swissprot;acc:q13418]	Subtracted	219.354	224.7	5.346	
1190	ubiquitin. [source:swissprot;acc:p02248]	Divided	209.6	204.372	1.02558	
1191	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	Subtracted	219.354	224.7	5.346	
1191	upstream binding protein 1 (lbp-1a). [source:refseq;acc:nm_014517]	Divided	220.742	215.237	1.02558	
1192	ras suppressor protein 1 (rsu-1) (rsp-1). [source:swissprot;acc:q15404]	Subtracted	219.354	224.7	5.346	
1192	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	Divided	220.742	215.237	1.02558	
1193	lbp-9. [source:refseq;acc:nm_014553]	Divided	220.742	215.237	1.02558	
1193	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [source:swissprot;acc:q13283]	Subtracted	219.354	224.7	5.346	
1194	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [source:swissprot;acc:q9un86]	Subtracted	219.354	224.7	5.346	
1194	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	Divided	220.742	215.237	1.02558	
1195	espin. [source:refseq;acc:nm_031475]	Subtracted	219.354	224.7	5.346	
1195	skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [source:swissprot;acc:q14192]	Divided	269.608	276.493	1.02554	
1196	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [source:swissprot;acc:p10635]	Subtracted	219.354	224.7	5.346	
1196	kinesin protein. [source:refseq;acc:nm_032559]	Divided	224.858	219.264	1.02551	
1197	mstp028 protein. [source:refseq;acc:nm_031954]	Divided	219.042	213.6	1.02548	
1197	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [source:refseq;acc:nm_006832]	Subtracted	219.354	224.7	5.346	
1198	lim and senescent cell antigen-like domains 2; ilk-binding protein. [source:refseq;acc:nm_017980]	Subtracted	219.354	224.7	5.346	
1198	skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [source:swissprot;acc:q13643]	Divided	269.59	276.454	1.02546	
1199	d(4) dopamine receptor (d(2c) dopamine receptor). [source:swissprot;acc:p21917]	Subtracted	219.354	224.7	5.346	
1199	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [source:swissprot;acc:o00566]	Divided	241.496	235.508	1.02543	
1200	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Subtracted	219.354	224.699	5.345	
1200	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [source:swissprot;acc:q12824]	Divided	219.03	213.604	1.0254	
1201	keratin associated protein 4-2; keratin associated protein 4.2. [source:refseq;acc:nm_033062]	Subtracted	219.354	224.699	5.345	
1201	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [source:swissprot;acc:p31040]	Divided	210.986	216.344	1.0254	
1202	diphthamide biosynthesis-like protein 2. [source:refseq;acc:nm_001384]	Divided	227.274	233.041	1.02537	
1202	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	Subtracted	219.354	224.699	5.345	
1203	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	Subtracted	219.354	224.699	5.345	
1203	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [source:swissprot;acc:q13829]	Divided	219.023	213.606	1.02536	
1204	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	Subtracted	219.354	224.699	5.345	
1204	polymerase delta-interacting protein 1; tnfaip1-like. [source:refseq;acc:nm_178863]	Divided	219.022	213.607	1.02535	
1205	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	Subtracted	219.354	224.699	5.345	
1205	ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	Divided	224.805	219.251	1.02533	
1206	integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	Divided	207.646	212.891	1.02526	
1206	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Subtracted	219.354	224.699	5.345	
1207	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	Subtracted	219.354	224.699	5.345	
1207	succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [source:swissprot;acc:q99643]	Divided	207.644	212.888	1.02525	
1208	keratin associated protein 1-3; keratin associated protein 1.3. [source:refseq;acc:nm_030966]	Subtracted	219.354	224.699	5.345	
1208	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	Divided	224.878	219.342	1.02524	
1209	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [source:swissprot;acc:p21912]	Divided	207.931	213.175	1.02522	
1209	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Subtracted	146.036	140.692	5.344	
1210	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	Subtracted	219.353	224.678	5.325	
1210	kinesin-like protein kif2 (kinesin-2) (hk2). [source:swissprot;acc:o00139]	Divided	224.764	219.241	1.02519	
1211	chromosome 11 open reading frame2; chromosome  11 open reading frame2. [source:refseq;acc:nm_013265]	Divided	214.364	219.759	1.02517	
1211	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Subtracted	174.387	179.697	5.31	
1212	coatomer gamma subunit (gamma-coat protein) (gamma-cop). [source:swissprot;acc:q9y678]	Subtracted	174.387	179.697	5.31	
1212	kinesin-like protein kif13a (kinesin-like protein rbkin). [source:swissprot;acc:q9h1h9]	Divided	214.364	219.759	1.02517	
1213	coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [source:swissprot;acc:q9y3c3]	Subtracted	174.387	179.697	5.31	
1213	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [source:swissprot;acc:q14746]	Divided	214.364	219.759	1.02517	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/