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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Filtered description Value Type Rank Gene green Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 14920 in total 
Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

description	Value Type	Rank	green	red	network_comparison	
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Squared	176	75.7214	48.5538	1.55954	
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [source:swissprot;acc:p78329]	Rooted	158	16.6919	14.2752	1.16929	
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Measured	148	379.474	293.178	1.29435	
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Ranked	134	10489.3	12314.9	1.17404	
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Squared	175	75.7214	48.5538	1.55954	
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [source:swissprot;acc:p98187]	Rooted	157	16.6919	14.2752	1.16929	
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Measured	132	56	42	1.33333	
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Ranked	203	15123	16853	1.1144	
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Squared	139	0.742249	0.417515	1.77778	
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	Rooted	171	7.48331	6.48074	1.1547	
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Measured	114	472.945	671.769	1.4204	
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Ranked	297	8719	8123.75	1.07327	
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Squared	164	91.0551	145.887	1.60218	
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [source:refseq;acc:nm_018959]	Rooted	136	20.1222	23.9877	1.1921	
dc11 protein. [source:refseq;acc:nm_020186]	Measured	180	681	556	1.22482	
dc11 protein. [source:refseq;acc:nm_020186]	Ranked	207	6716	7479	1.11361	
dc11 protein. [source:refseq;acc:nm_020186]	Squared	178	109.766	73.1683	1.50019	
dc11 protein. [source:refseq;acc:nm_020186]	Rooted	250	26.096	23.5797	1.10671	
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Measured	327	161.091	175.644	1.09034	
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Ranked	372	12402.7	11869.9	1.04489	
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Squared	393	8.43969	9.11845	1.08042	
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Rooted	301	11.8854	12.7534	1.07303	
dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Measured	109	144	100	1.44	
dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Ranked	176	11528	13068	1.13359	
dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Squared	105	4.90793	2.36686	2.0736	
dead-box protein abstrakt homolog. [source:swissprot;acc:q9ujv9]	Rooted	134	12	10	1.2	
dead-box protein. [source:refseq;acc:nm_018665]	Measured	76	183	313.667	1.71403	
dead-box protein. [source:refseq;acc:nm_018665]	Ranked	58	14486	10628.3	1.36296	
dead-box protein. [source:refseq;acc:nm_018665]	Squared	116	19.3759	37.7545	1.94853	
dead-box protein. [source:refseq;acc:nm_018665]	Rooted	57	10.8929	16.237	1.4906	
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	Measured	476	1372.31	1362.55	1.00716	
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	Ranked	326	11295.6	11948.4	1.05779	
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	Squared	488	5469.34	5487.61	1.00334	
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [source:refseq;acc:nm_030655]	Rooted	401	22.6039	21.8861	1.0328	
deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Measured	48	403.196	870.482	2.15895	
deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Ranked	80	11617.9	9102.34	1.27636	
deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Squared	55	113.017	468.221	4.14293	
deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	Rooted	55	16.281	24.4683	1.50287	
dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Measured	463	1248.14	1262.65	1.01163	
dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Ranked	164	10412.4	11971.7	1.14975	
dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Squared	295	3268.89	3966.2	1.21332	
dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	Rooted	237	23.7622	21.2911	1.11606	
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Measured	200	482.7	578.056	1.19755	
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Ranked	344	10027.6	10540.6	1.05116	
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Squared	128	90.363	166.774	1.8456	
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [source:swissprot;acc:q12882]	Rooted	441	19.441	19.9002	1.02362	
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Measured	321	686.693	628.072	1.09333	
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Ranked	103	9130.38	7495.26	1.21815	
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Squared	126	219.216	118.204	1.85456	
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [source:swissprot;acc:p31513]	Rooted	296	22.454	24.1524	1.07564	

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/