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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Value Type description Interaction Map Rank Network Comparison Type red Gene Filtered green network_comparison

Results: HTML CSV LaTeX

Showing element 1875 to 1924 of 3228 in total

Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [source:swissprot;acc:p13662]	3113	0.00001	0.00001	1	
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [source:swissprot;acc:p16991]	2094	6682.05	7051.02	1.05522	
nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	937	5859.25	6432.03	1.09776	
nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	939	5859.25	6432.03	1.09776	
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	428	3721.19	4288.17	1.15237	
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [source:swissprot;acc:q14978]	2842	0.00001	0.00001	1	
nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	213	4446.72	5553.79	1.24896	
nucleolar protein family a, member 2; component of the h/aca snornp. [source:refseq;acc:nm_017838]	997	5144.74	5634	1.0951	
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	1121	4338.49	4725.86	1.08929	
nucleolar protein nop56 (nucleolar protein 5a). [source:swissprot;acc:o00567]	619	3879.99	4371.24	1.12661	
nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	755	4079.81	4545.01	1.11402	
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	80	4133.47	5945.32	1.43834	
nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	81	4136.36	5943.56	1.43691	
nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [source:swissprot;acc:p06748]	2785	0.00001	0.00001	1	
nucleoplasmin 3. [source:swissprot;acc:o75607]	3096	0.00001	0.00001	1	
nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [source:swissprot;acc:q9ukx7]	3154	0.00001	0.00001	1	
nucleoporin 54kda; nucleoporin p54. [source:refseq;acc:nm_017426]	1999	5047.2	5344.68	1.05894	
nucleoporin like 1. [source:refseq;acc:nm_014089]	1993	6174.74	6538.73	1.05895	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	2430	7243.07	7509.58	1.0368	
nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [source:swissprot;acc:p52594]	2557	5291.65	5187.78	1.02002	
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	618	7878.27	8879.08	1.12703	
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [source:swissprot;acc:p15531]	638	7755.69	8730.74	1.12572	
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [source:swissprot;acc:p22392]	639	7753.59	8728.13	1.12569	
nucleosome assembly protein 1-like 1 (nap-1 related protein). [source:swissprot;acc:p55209]	2757	0.00001	0.00001	1	
nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [source:swissprot;acc:q9ulw6]	2758	0.00001	0.00001	1	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	3080	0.00001	0.00001	1	
nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	446	3766.03	4329.37	1.14958	
nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	293	4641.09	5588.75	1.20419	
nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]	292	4641.09	5588.75	1.20419	
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	2373	3677.53	3526.65	1.04278	
numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	665	6374.65	7145.59	1.12094	
numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	669	6374.65	7145.59	1.12094	
ny-ren-24 antigen (fragment). [source:sptrembl;acc:q9y5a4]	2624	6815.24	6916.14	1.01481	
ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	1103	5358.18	5843.73	1.09062	
o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	1004	5391.64	5903.72	1.09498	
odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	305	3856.29	4624.15	1.19912	
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	2744	10143.6	10163.6	1.00197	
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	2742	10198.1	10174.3	1.00234	
oligophrenin 1. [source:swissprot;acc:o60890]	2688	3953.53	3972.32	1.00475	
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	2686	3953.53	3972.32	1.00475	
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [source:swissprot;acc:q9y3b8]	1138	5790.65	6303.92	1.08864	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	189	4571.89	5864.86	1.28281	
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [source:swissprot;acc:q14982]	924	5406.5	5939.42	1.09857	
opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	2566	3964.71	4042.75	1.01968	
origin recognition complex subunit 2. [source:swissprot;acc:q13416]	3047	0.00001	0.00001	1	
origin recognition complex subunit 5. [source:swissprot;acc:o43913]	2851	0.00001	0.00001	1	
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	1470	5473.09	5887.45	1.07571	
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	1355	5783.9	6240.19	1.07889	
ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	817	6811.2	7547.35	1.10808	
ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	819	6805.45	7540.5	1.10801	

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/