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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Network Comparison Type description Value Type Interaction Map red Filtered network_comparison green
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	network_comparison	green	
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	1.02187	211.908	
1376	eyes absent homolog 3. [source:swissprot;acc:q99504]	218.537	1.02163	213.91	
1377	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	218.471	1.02148	213.876	
1378	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	218.47	1.02148	213.876	
1379	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	218.47	1.02148	213.875	
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	1.02148	213.876	
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	1.02148	213.876	
1382	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	218.47	1.02148	213.876	
1383	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	218.47	1.02148	213.876	
1384	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	218.471	1.02148	213.876	
1385	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	218.47	1.02148	213.875	
1386	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	218.47	1.02148	213.876	
1387	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	218.47	1.02148	213.875	
1388	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	218.471	1.02148	213.876	
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	1.02148	213.875	
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	1.02148	213.875	
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	218.47	1.02148	213.875	
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	218.471	1.02148	213.876	
1393	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	218.47	1.02148	213.875	
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	1.02148	213.875	
1395	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	218.47	1.02148	213.876	
1396	eyes absent homolog 1. [source:swissprot;acc:q99502]	218.463	1.02147	213.872	
1397	40s ribosomal protein s8. [source:swissprot;acc:p09058]	218.64	1.02145	214.049	
1398	eyes absent homolog 4. [source:swissprot;acc:o95677]	218.449	1.02144	213.864	
1399	eyes absent homolog 2. [source:swissprot;acc:o00167]	218.417	1.02137	213.848	
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	218.667	1.02125	214.118	
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	1.02124	214.11	
1402	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	209.682	1.0212	205.329	
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	1.0212	180.823	
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	1.02104	237.65	
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	245.532	1.021	240.483	
1406	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	212.833	1.021	208.456	
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	1.02096	210.424	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	206.102	1.02095	210.42	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	206.102	1.02095	210.42	
1410	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	206.1	1.02095	210.417	
1411	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	206.102	1.02095	210.42	
1412	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	206.102	1.02095	210.42	
1413	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	206.102	1.02095	210.42	
1414	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [source:refseq;acc:nm_138393]	206.102	1.02095	210.42	
1415	stromal interaction molecule 2 precursor. [source:swissprot;acc:q9p246]	206.102	1.02095	210.42	
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	1.02095	210.42	
1417	carboxypeptidase a5. [source:refseq;acc:nm_080385]	203.979	1.02084	208.229	
1418	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	203.979	1.02084	208.229	
1419	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	203.979	1.02084	208.229	
1420	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	203.979	1.02084	208.229	
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	1.02084	211.391	
1422	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	203.979	1.02084	208.229	
1423	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [source:swissprot;acc:p50238]	221.152	1.02074	216.659	
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	1.02068	219.157	

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/