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 green red network_comparison
Results: HTML CSV LaTeX Showing element 1858 to 1907 of 3730 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
1356	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848]	223.475	228.409	1.02208	
1357	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	223.475	228.409	1.02208	
1358	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	210.359	214.987	1.022	
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	223.726	228.642	1.02197	
1360	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [source:swissprot;acc:p36897]	228.805	223.89	1.02195	
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	210.354	214.971	1.02195	
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	223.736	228.644	1.02194	
1363	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	213.899	218.591	1.02194	
1364	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [source:swissprot;acc:p36896]	228.797	223.885	1.02194	
1365	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	223.736	228.644	1.02194	
1366	activin a receptor, type ic; activin receptor-like kinase 7. [source:refseq;acc:nm_145259]	228.795	223.884	1.02194	
1367	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610]	228.799	223.887	1.02194	
1368	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	223.736	228.644	1.02194	
1369	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	223.736	228.644	1.02194	
1370	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	200.784	205.185	1.02192	
1371	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	223.744	228.646	1.02191	
1372	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	211.908	216.542	1.02187	
1373	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	211.908	216.542	1.02187	
1374	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	211.908	216.542	1.02187	
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]	211.908	216.542	1.02187	
1376	eyes absent homolog 3. [source:swissprot;acc:q99504]	213.91	218.537	1.02163	
1377	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	213.876	218.471	1.02148	
1378	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	213.876	218.47	1.02148	
1379	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	213.875	218.47	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]	213.876	218.47	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]	213.876	218.47	1.02148	
1382	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	213.876	218.47	1.02148	
1383	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	213.876	218.47	1.02148	
1384	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	213.876	218.471	1.02148	
1385	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	213.875	218.47	1.02148	
1386	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	213.876	218.47	1.02148	
1387	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	213.875	218.47	1.02148	
1388	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	213.876	218.471	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]	213.875	218.47	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]	213.875	218.47	1.02148	
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	213.875	218.47	1.02148	
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	213.876	218.471	1.02148	
1393	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	213.875	218.47	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]	213.875	218.47	1.02148	
1395	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	213.876	218.47	1.02148	
1396	eyes absent homolog 1. [source:swissprot;acc:q99502]	213.872	218.463	1.02147	
1397	40s ribosomal protein s8. [source:swissprot;acc:p09058]	214.049	218.64	1.02145	
1398	eyes absent homolog 4. [source:swissprot;acc:o95677]	213.864	218.449	1.02144	
1399	eyes absent homolog 2. [source:swissprot;acc:o00167]	213.848	218.417	1.02137	
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	214.118	218.667	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]	214.11	218.657	1.02124	
1402	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	205.329	209.682	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]	180.823	184.656	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]	237.65	232.752	1.02104	
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	240.483	245.532	1.021	

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/