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 2680 to 2729 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1340	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	Subtracted	218.47	213.875	4.595	
1341	eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [source:swissprot;acc:p05198]	Divided	226.433	231.491	1.02234	
1341	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599]	Subtracted	218.47	213.875	4.595	
1342	histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [source:swissprot;acc:o43463]	Divided	226.433	231.491	1.02234	
1342	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	Subtracted	218.47	213.876	4.594	
1343	m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [source:swissprot;acc:p30304]	Divided	258.558	252.916	1.02231	
1343	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]	Subtracted	218.47	213.876	4.594	
1344	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [source:refseq;acc:nm_006027]	Divided	216.772	221.594	1.02224	
1344	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]	Subtracted	218.47	213.876	4.594	
1345	phd finger protein 9. [source:refseq;acc:nm_018062]	Divided	216.772	221.594	1.02224	
1345	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	Subtracted	218.47	213.876	4.594	
1346	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	Subtracted	218.47	213.876	4.594	
1346	small optic lobes homolog; small optic lobes, drosophila, homolog of. [source:refseq;acc:nm_005632]	Divided	216.772	221.594	1.02224	
1347	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	Divided	204.961	209.517	1.02223	
1347	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	Subtracted	218.47	213.876	4.594	
1348	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	Subtracted	218.47	213.876	4.594	
1348	zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [source:swissprot;acc:q15915]	Divided	218.569	213.832	1.02215	
1349	40s ribosomal protein s8. [source:swissprot;acc:p09058]	Subtracted	218.64	214.049	4.591	
1349	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [source:swissprot;acc:o60481]	Divided	218.572	213.841	1.02212	
1350	eyes absent homolog 1. [source:swissprot;acc:q99502]	Subtracted	218.463	213.872	4.591	
1350	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [source:swissprot;acc:o95409]	Divided	218.574	213.847	1.0221	
1351	eyes absent homolog 4. [source:swissprot;acc:o95677]	Subtracted	218.449	213.864	4.585	
1351	prohibitin. [source:swissprot;acc:p35232]	Divided	211.513	206.941	1.02209	
1352	prohibitin. [source:swissprot;acc:p35232]	Subtracted	211.513	206.941	4.572	
1352	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Divided	211.513	206.941	1.02209	
1353	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849]	Divided	228.409	223.475	1.02208	
1353	repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	Subtracted	211.513	206.941	4.572	
1354	eyes absent homolog 2. [source:swissprot;acc:o00167]	Subtracted	218.417	213.848	4.569	
1354	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	Divided	228.409	223.475	1.02208	
1355	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [source:swissprot;acc:o43766]	Subtracted	204.961	209.517	4.556	
1355	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	Divided	228.409	223.475	1.02208	
1356	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	Subtracted	218.667	214.118	4.549	
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]	Divided	228.409	223.475	1.02208	
1357	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336]	Subtracted	218.657	214.11	4.547	
1357	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	Divided	228.409	223.475	1.02208	
1358	geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [source:swissprot;acc:p53609]	Subtracted	225.039	229.573	4.534	
1358	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	Divided	214.987	210.359	1.022	
1359	fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [source:refseq;acc:nm_021727]	Subtracted	225.039	229.573	4.534	
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	Divided	228.642	223.726	1.02197	
1360	mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [source:swissprot;acc:q13485]	Subtracted	225.039	229.573	4.534	
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]	Divided	223.89	228.805	1.02195	
1361	fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [source:refseq;acc:nm_004265]	Subtracted	225.039	229.573	4.534	
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	Divided	214.971	210.354	1.02195	
1362	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [source:refseq;acc:nm_013402]	Subtracted	225.039	229.573	4.534	
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	Divided	228.644	223.736	1.02194	
1363	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	Divided	218.591	213.899	1.02194	
1363	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	Subtracted	168.989	164.46	4.529	
1364	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	Subtracted	168.995	164.467	4.528	
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]	Divided	223.885	228.797	1.02194	
1365	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	Divided	228.644	223.736	1.02194	

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/