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 red green network_comparison
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1329	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [source:sptrembl;acc:q9h4v7]	Divided	218.509	213.648	1.02275	
1330	calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [source:swissprot;acc:p53805]	Divided	218.508	213.648	1.02275	
1330	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	Subtracted	218.471	213.876	4.595	
1331	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	Subtracted	218.47	213.875	4.595	
1331	calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [source:swissprot;acc:q9uka8]	Divided	218.509	213.649	1.02275	
1332	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	Subtracted	218.471	213.876	4.595	
1332	cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [source:swissprot;acc:q15070]	Divided	220.681	215.78	1.02271	
1333	60s ribosomal protein l34, mitochondrial precursor (l34mt). [source:swissprot;acc:q9bq48]	Divided	220.681	215.78	1.02271	
1333	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Subtracted	218.47	213.875	4.595	
1334	jm4 protein. [source:refseq;acc:nm_007213]	Divided	199.643	204.163	1.02264	
1334	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	Subtracted	218.47	213.875	4.595	
1335	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [source:refseq;acc:nm_006407]	Divided	199.771	204.287	1.02261	
1335	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	Subtracted	218.471	213.876	4.595	
1336	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]	Subtracted	218.47	213.875	4.595	
1336	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	Divided	215.162	210.412	1.02257	
1337	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [source:refseq;acc:nm_013316]	Subtracted	218.47	213.875	4.595	
1337	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	Divided	215.162	210.412	1.02257	
1338	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	Subtracted	218.47	213.875	4.595	
1338	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	Divided	215.162	210.412	1.02257	
1339	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	Subtracted	218.471	213.876	4.595	
1339	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	Divided	205.204	200.71	1.02239	
1340	histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [source:swissprot;acc:q9h5i1]	Divided	226.433	231.491	1.02234	
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	

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/