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

Rank	description	network_comparison	green	red	
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]	1.02187	211.908	216.542	
1376	eyes absent homolog 3. [source:swissprot;acc:q99504]	1.02163	213.91	218.537	
1377	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	1.02148	213.876	218.471	
1378	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	1.02148	213.876	218.47	
1379	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	1.02148	213.875	218.47	
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]	1.02148	213.876	218.47	
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]	1.02148	213.876	218.47	
1382	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	1.02148	213.876	218.47	
1383	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	1.02148	213.876	218.47	
1384	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	1.02148	213.876	218.471	
1385	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	1.02148	213.875	218.47	
1386	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	1.02148	213.876	218.47	
1387	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	1.02148	213.875	218.47	
1388	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	1.02148	213.876	218.471	
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]	1.02148	213.875	218.47	
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]	1.02148	213.875	218.47	
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	1.02148	213.875	218.47	
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	1.02148	213.876	218.471	
1393	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	1.02148	213.875	218.47	
1394	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599]	1.02148	213.875	218.47	
1395	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	1.02148	213.876	218.47	
1396	eyes absent homolog 1. [source:swissprot;acc:q99502]	1.02147	213.872	218.463	
1397	40s ribosomal protein s8. [source:swissprot;acc:p09058]	1.02145	214.049	218.64	
1398	eyes absent homolog 4. [source:swissprot;acc:o95677]	1.02144	213.864	218.449	
1399	eyes absent homolog 2. [source:swissprot;acc:o00167]	1.02137	213.848	218.417	
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	1.02125	214.118	218.667	
1401	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336]	1.02124	214.11	218.657	
1402	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	1.0212	205.329	209.682	
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]	1.0212	180.823	184.656	
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]	1.02104	237.65	232.752	
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	1.021	240.483	245.532	
1406	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	1.021	208.456	212.833	
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]	1.02096	210.424	206.104	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	1.02095	210.42	206.102	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	1.02095	210.42	206.102	
1410	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	1.02095	210.417	206.1	
1411	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	1.02095	210.42	206.102	
1412	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	1.02095	210.42	206.102	
1413	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	1.02095	210.42	206.102	
1414	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	1.02095	210.42	206.102	
1415	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	1.02095	210.42	206.102	
1416	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [source:swissprot;acc:q9p286]	1.02095	210.42	206.102	
1417	carboxypeptidase a5. [source:refseq;acc:nm_080385]	1.02084	208.229	203.979	
1418	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	1.02084	208.229	203.979	
1419	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	1.02084	208.229	203.979	
1420	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	1.02084	208.229	203.979	
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]	1.02084	211.391	207.076	
1422	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	1.02084	208.229	203.979	
1423	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [source:swissprot;acc:p50238]	1.02074	216.659	221.152	
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]	1.02068	219.157	214.717	

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/