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 2430 to 2479 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1215	peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [source:swissprot;acc:q9unp9]	Subtracted	174.387	179.697	5.31	
1216	coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [source:swissprot;acc:q9p299]	Subtracted	174.387	179.697	5.31	
1216	retinoic acid induced 17; pias-like protein hzimp10. [source:refseq;acc:nm_020338]	Divided	218.269	212.918	1.02513	
1217	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [source:refseq;acc:nm_018292]	Divided	211.959	217.258	1.025	
1217	hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [source:swissprot;acc:q92819]	Subtracted	221.093	226.399	5.306	
1218	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	Divided	211.959	217.258	1.025	
1218	hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [source:swissprot;acc:q92839]	Subtracted	221.093	226.399	5.306	
1219	coactosin-like protein. [source:swissprot;acc:q14019]	Divided	211.959	217.258	1.025	
1219	hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [source:swissprot;acc:o00219]	Subtracted	221.093	226.399	5.306	
1220	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [source:refseq;acc:nm_018292]	Subtracted	211.959	217.258	5.299	
1220	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	Divided	211.959	217.258	1.025	
1221	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	Subtracted	211.959	217.258	5.299	
1221	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	Divided	211.959	217.258	1.025	
1222	coactosin-like protein. [source:swissprot;acc:q14019]	Subtracted	211.959	217.258	5.299	
1222	tumor protein d53 (hd53) (d52-like 1). [source:swissprot;acc:q16890]	Divided	206.774	211.936	1.02496	
1223	tumor protein d52 (n8 protein). [source:swissprot;acc:p55327]	Divided	206.771	211.926	1.02493	
1223	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	Subtracted	211.959	217.258	5.299	
1224	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [source:swissprot;acc:q05932]	Divided	225.906	231.524	1.02487	
1224	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	Subtracted	211.959	217.258	5.299	
1225	interleukin-4 induced protein 1 precursor (fig-1 protein). [source:swissprot;acc:q96rq9]	Subtracted	219.55	214.288	5.262	
1225	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	Divided	166.846	170.989	1.02483	
1226	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [source:swissprot;acc:p10109]	Subtracted	191.139	185.882	5.257	
1226	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	Divided	166.846	170.989	1.02483	
1227	glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [source:swissprot;acc:p48507]	Subtracted	213.079	218.325	5.246	
1227	pyrroline 5-carboxylate reductase isoform. [source:refseq;acc:nm_013328]	Divided	172.365	168.219	1.02465	
1228	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [source:swissprot;acc:p48506]	Subtracted	213.079	218.325	5.246	
1228	glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [source:swissprot;acc:p48507]	Divided	213.079	218.325	1.02462	
1229	glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [source:swissprot;acc:p48506]	Divided	213.079	218.325	1.02462	
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	

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/