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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 2458 to 2507 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1229	integral membrane protein cii-3b. [source:sptrembl;acc:o75609]	Subtracted	207.646	212.891	5.245	
1230	interleukin-4 induced protein 1 precursor (fig-1 protein). [source:swissprot;acc:q96rq9]	Divided	219.55	214.288	1.02456	
1230	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]	Subtracted	207.644	212.888	5.244	
1231	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Divided	212.724	207.637	1.0245	
1231	succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [source:swissprot;acc:p21912]	Subtracted	207.931	213.175	5.244	
1232	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [source:swissprot;acc:p19652]	Subtracted	209.649	204.406	5.243	
1232	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [source:swissprot;acc:p32322]	Divided	172.543	168.417	1.0245	
1233	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Divided	212.724	207.637	1.0245	
1233	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Subtracted	142.077	136.846	5.231	
1234	phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [source:swissprot;acc:p15259]	Divided	212.724	207.637	1.0245	
1234	ubiquitin. [source:swissprot;acc:p02248]	Subtracted	209.6	204.372	5.228	
1235	coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [source:swissprot;acc:p53621]	Subtracted	177.432	182.647	5.215	
1235	keratin associated protein 9-4; keratin associated protein 9.4. [source:refseq;acc:nm_033191]	Divided	219.356	224.723	1.02447	
1236	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	Divided	219.354	224.699	1.02437	
1236	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [source:swissprot;acc:q15765]	Subtracted	226.439	221.26	5.179	
1237	keratin associated protein 4-2; keratin associated protein 4.2. [source:refseq;acc:nm_033062]	Divided	219.354	224.699	1.02437	
1237	prefoldin subunit 2 (hspc231). [source:swissprot;acc:q9uhv9]	Subtracted	226.439	221.26	5.179	
1238	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	Divided	219.354	224.699	1.02437	
1238	uxt protein (ubiquitously expressed transcript protein) (hspc024). [source:swissprot;acc:q9ubk9]	Subtracted	226.439	221.26	5.179	
1239	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	Divided	219.354	224.699	1.02437	
1239	signal transducer and activator of transcription 4. [source:swissprot;acc:q14765]	Subtracted	222.573	227.751	5.178	
1240	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	Divided	219.354	224.7	1.02437	
1240	signal transducer and activator of transcription 1-alpha/beta (transcription factor isgf-3 components p91/p84). [source:swissprot;acc:p42224]	Subtracted	222.574	227.752	5.178	
1241	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	Divided	219.354	224.7	1.02437	
1241	signal transducer and activator of transcription 3 (acute-phase response factor). [source:swissprot;acc:p40763]	Subtracted	222.573	227.75	5.177	
1242	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	Divided	219.354	224.7	1.02437	
1242	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [source:swissprot;acc:q12967]	Subtracted	162.055	156.884	5.171	
1243	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	Divided	219.354	224.699	1.02437	
1243	signal transducer and activator of transcription 6 (il-4 stat). [source:swissprot;acc:p42226]	Subtracted	222.569	227.739	5.17	
1244	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	Divided	219.354	224.7	1.02437	
1244	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	Subtracted	206.774	211.936	5.162	
1245	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	Divided	219.354	224.699	1.02437	
1245	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	Subtracted	206.771	211.926	5.155	
1246	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	Divided	219.354	224.699	1.02437	
1246	sestrin 3. [source:swissprot;acc:p58005]	Subtracted	218.368	213.219	5.149	
1247	sestrin 2 (hi95). [source:swissprot;acc:p58004]	Subtracted	218.368	213.219	5.149	
1247	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	Divided	219.354	224.7	1.02437	
1248	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [source:swissprot;acc:q02928]	Subtracted	218.368	213.22	5.148	
1248	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	Divided	219.354	224.699	1.02437	
1249	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	Divided	219.354	224.7	1.02437	
1249	cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:q08477]	Subtracted	218.368	213.22	5.148	
1250	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Subtracted	218.368	213.22	5.148	
1250	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [source:swissprot;acc:p48059]	Divided	219.354	224.7	1.02437	
1251	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [source:swissprot;acc:q13418]	Divided	219.354	224.7	1.02437	
1251	likely ortholog of rat cytochrome p450 4x1. [source:refseq;acc:nm_178033]	Subtracted	218.368	213.22	5.148	
1252	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [source:swissprot;acc:q9hcs2]	Subtracted	218.368	213.22	5.148	
1252	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	Divided	219.354	224.7	1.02437	
1253	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Subtracted	218.368	213.22	5.148	
1253	ras suppressor protein 1 (rsu-1) (rsp-1). [source:swissprot;acc:q15404]	Divided	219.354	224.7	1.02437	
1254	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [source:swissprot;acc:q9hbi6]	Subtracted	218.368	213.22	5.148	

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/