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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1375 to 1424 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1375	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	216.542	211.908	1.02187	
1376	eyes absent homolog 3. [source:swissprot;acc:q99504]	218.537	213.91	1.02163	
1377	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	218.471	213.876	1.02148	
1378	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	218.47	213.876	1.02148	
1379	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	218.47	213.875	1.02148	
1380	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [source:swissprot;acc:p40818]	218.47	213.876	1.02148	
1381	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [source:refseq;acc:nm_005156]	218.47	213.876	1.02148	
1382	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	218.47	213.876	1.02148	
1383	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	218.47	213.876	1.02148	
1384	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	218.471	213.876	1.02148	
1385	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	218.47	213.875	1.02148	
1386	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	218.47	213.876	1.02148	
1387	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	218.47	213.875	1.02148	
1388	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	218.471	213.876	1.02148	
1389	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	218.47	213.875	1.02148	
1390	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [source:refseq;acc:nm_013316]	218.47	213.875	1.02148	
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	218.47	213.875	1.02148	
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	218.471	213.876	1.02148	
1393	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	218.47	213.875	1.02148	
1394	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599]	218.47	213.875	1.02148	
1395	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	218.47	213.876	1.02148	
1396	eyes absent homolog 1. [source:swissprot;acc:q99502]	218.463	213.872	1.02147	
1397	40s ribosomal protein s8. [source:swissprot;acc:p09058]	218.64	214.049	1.02145	
1398	eyes absent homolog 4. [source:swissprot;acc:o95677]	218.449	213.864	1.02144	
1399	eyes absent homolog 2. [source:swissprot;acc:o00167]	218.417	213.848	1.02137	
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	218.667	214.118	1.02125	
1401	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336]	218.657	214.11	1.02124	
1402	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	209.682	205.329	1.0212	
1403	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	184.656	180.823	1.0212	
1404	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	232.752	237.65	1.02104	
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	245.532	240.483	1.021	
1406	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	212.833	208.456	1.021	
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [source:refseq;acc:nm_020830]	206.104	210.424	1.02096	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	206.102	210.42	1.02095	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	206.102	210.42	1.02095	
1410	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	206.1	210.417	1.02095	
1411	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	206.102	210.42	1.02095	
1412	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	206.102	210.42	1.02095	
1413	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	206.102	210.42	1.02095	
1414	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	206.102	210.42	1.02095	
1415	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	206.102	210.42	1.02095	
1416	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [source:swissprot;acc:q9p286]	206.102	210.42	1.02095	
1417	carboxypeptidase a5. [source:refseq;acc:nm_080385]	203.979	208.229	1.02084	
1418	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	203.979	208.229	1.02084	
1419	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	203.979	208.229	1.02084	
1420	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	203.979	208.229	1.02084	
1421	acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [source:swissprot;acc:q13510]	207.076	211.391	1.02084	
1422	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	203.979	208.229	1.02084	
1423	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [source:swissprot;acc:p50238]	221.152	216.659	1.02074	
1424	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	214.717	219.157	1.02068	

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/