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

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Showing element 3180 to 3229 of 38536 in total

Filtered	0
Network Comparison Type	Divided

description	green	Value Type	Rank	network_comparison	Interaction Map	red	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	4871.6	Ranked	35	1.5182	High confidence	3208.8	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	19621.3	Measured	180	1.21389	Low confidence	23818.1	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	19621.3	Measured	193	1.21389	High confidence	23818.1	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	160184	Squared	170	1.45125	Low confidence	232467	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	160184	Squared	189	1.45125	High confidence	232467	
nuclear lim interactor-interacting factor 1 (nli-interacting factor 1) (nif-like protein) (ya22 protein) (hya22). [source:swissprot;acc:o15194]	18.5623	Rooted	376	1.09168	Low confidence	17.0034	
nuclear lim interactor-interacting factor 1 (nli-interacting factor 1) (nif-like protein) (ya22 protein) (hya22). [source:swissprot;acc:o15194]	480.337	Squared	191	1.36578	Low confidence	656.037	
nuclear lim interactor-interacting factor 1 (nli-interacting factor 1) (nif-like protein) (ya22 protein) (hya22). [source:swissprot;acc:o15194]	718.102	Measured	607	1.0351	Low confidence	693.753	
nuclear lim interactor-interacting factor 1 (nli-interacting factor 1) (nif-like protein) (ya22 protein) (hya22). [source:swissprot;acc:o15194]	11938.2	Ranked	435	1.07486	Low confidence	12831.9	
nuclear lim interactor-interacting factor 2 (nli-interacting factor 2) (protein os-4). [source:swissprot;acc:o14595]	18.664	Rooted	380	1.08993	Low confidence	17.1241	
nuclear lim interactor-interacting factor 2 (nli-interacting factor 2) (protein os-4). [source:swissprot;acc:o14595]	483.747	Squared	190	1.36579	Low confidence	660.695	
nuclear lim interactor-interacting factor 2 (nli-interacting factor 2) (protein os-4). [source:swissprot;acc:o14595]	723.073	Measured	610	1.03491	Low confidence	698.679	
nuclear lim interactor-interacting factor 2 (nli-interacting factor 2) (protein os-4). [source:swissprot;acc:o14595]	11891	Ranked	446	1.07363	Low confidence	12766.5	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	0.00001	Measured	95	15400000	High confidence	154	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	0.00001	Squared	2	561325	High confidence	5.61325	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	0.00001	Rooted	2	1240970	High confidence	12.4097	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	22.9582	Rooted	720	1.0168	Low confidence	23.3438	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	1330.95	Measured	664	1.02444	Low confidence	1363.48	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	3698.75	Squared	285	1.19319	Low confidence	4413.3	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	11256.8	Ranked	819	1.002	Low confidence	11234.3	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	21888	Ranked	8	1.89918	High confidence	11525	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	27.2079	Rooted	415	1.07835	Low confidence	29.3397	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	27.9904	Rooted	219	1.13456	High confidence	31.7569	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	1921.25	Measured	640	1.02757	Low confidence	1974.21	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	2668.56	Measured	458	1.01327	High confidence	2633.61	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	6622.06	Squared	823	1.00289	Low confidence	6603	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	9878.65	Squared	391	1.08482	High confidence	9106.26	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	11164.2	Ranked	310	1.11276	Low confidence	10032.9	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	12106.5	Ranked	79	1.27901	High confidence	9465.55	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	70.9983	Rooted	172	1.15183	Low confidence	61.6393	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	70.9983	Rooted	175	1.15183	High confidence	61.6393	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	5700.79	Ranked	47	1.31395	Low confidence	4338.65	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	5700.79	Ranked	71	1.31395	High confidence	4338.65	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	7500.75	Measured	103	1.46874	Low confidence	5106.93	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	7500.75	Measured	104	1.46874	High confidence	5106.93	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	23426.5	Squared	97	2.23326	High confidence	10489.8	
nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	23426.5	Squared	97	2.23326	Low confidence	10489.8	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	23.7041	Rooted	502	1.0542	Low confidence	24.9889	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	29.828	Rooted	73	1.36418	High confidence	21.8651	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	952.74	Squared	376	1.11487	High confidence	1062.18	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	1397.66	Measured	188	1.22221	High confidence	1143.55	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	1596.65	Measured	470	1.07112	Low confidence	1710.21	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	6643.86	Squared	319	1.15612	Low confidence	7681.13	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	8691.76	Ranked	33	1.52929	High confidence	13292.2	
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]	11587.2	Ranked	604	1.03567	Low confidence	11188.1	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	21.9983	Rooted	66	1.40854	High confidence	30.9855	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	49.9102	Rooted	459	1.06557	Low confidence	53.1828	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	509.542	Squared	73	2.9342	High confidence	1495.1	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	925.298	Measured	75	1.71412	High confidence	1586.07	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	4646.41	Measured	750	1.01235	Low confidence	4703.81	

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/