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

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Showing element 501 to 550 of 38536 in total

Network Comparison Type	Divided

description	Filtered	green	Value Type	network_comparison	Rank	Interaction Map	red	
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]	1	73.5484	Rooted	1.02832	3855	Low confidence	71.5231	
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]	1	200.093	Ranked	1.01094	4091	Low confidence	202.282	
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]	1	8094.29	Measured	1.02451	3728	Low confidence	7900.62	
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]	1	43022.5	Squared	1.04104	1886	Low confidence	44788.1	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	69.3348	Rooted	1.03153	1764	High confidence	67.2158	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	88.7007	Rooted	1.04795	399	Low confidence	84.6421	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	176.667	Ranked	1.02263	1250	Low confidence	180.665	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	208.162	Ranked	1.00662	2189	High confidence	209.54	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	7295.24	Measured	1.05481	2105	High confidence	6916.14	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	11639.5	Measured	1.08815	143	Low confidence	10696.6	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	36579.1	Squared	1.0287	2642	High confidence	35558.6	
3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [source:swissprot;acc:p46952]	1	74962.3	Squared	1.15248	111	Low confidence	65044.3	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	25.4539	Rooted	1.06963	442	Low confidence	27.2263	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	31.1453	Rooted	1.03923	376	High confidence	32.3671	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	1932.95	Measured	1.04278	581	Low confidence	2015.65	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	2853.65	Measured	1.0252	438	High confidence	2925.57	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	10466.5	Ranked	1.05751	327	High confidence	9897.29	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	10485.1	Squared	1.03494	703	Low confidence	10851.4	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	11352.1	Ranked	1.0588	501	Low confidence	10721.7	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	0	18218.3	Squared	1.0074	477	High confidence	18353.1	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	71.371	Rooted	1.01481	2412	High confidence	70.3295	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	74.3827	Rooted	1.03876	1052	Low confidence	71.6074	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	198.154	Ranked	1.01095	1852	High confidence	196.008	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	198.284	Ranked	1.02557	879	Low confidence	203.354	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	7317.48	Measured	1.0628	1898	High confidence	6885.11	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	8232.52	Measured	1.0334	1660	Low confidence	7966.46	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	32866.2	Squared	1.17808	646	High confidence	27898	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1	43619.2	Squared	1.03355	3343	Low confidence	45082.7	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	24.5318	Rooted	1.0647	461	Low confidence	26.1189	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	26.8141	Rooted	1.04688	357	High confidence	28.0711	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	1500.63	Measured	1.07746	459	Low confidence	1616.87	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	1721.76	Measured	1.06708	346	High confidence	1837.26	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	5250.39	Squared	1.05066	655	Low confidence	5516.4	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	6794.39	Squared	1.02587	455	High confidence	6970.13	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	10243.1	Ranked	1.00854	478	High confidence	10156.4	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	0	10984.2	Ranked	1.03221	614	Low confidence	10641.4	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	72.2607	Rooted	1.01145	2490	High confidence	71.4427	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	75.8932	Rooted	1.02825	3866	Low confidence	73.8081	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	192.486	Ranked	1.01776	2649	Low confidence	195.904	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	192.541	Ranked	1.00511	2300	High confidence	191.563	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	7263.87	Measured	1.04564	2305	High confidence	6946.82	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	8366.35	Measured	1.02419	3780	Low confidence	8168.73	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	31125.2	Squared	1.14283	1116	High confidence	27235.1	
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]	1	43332.8	Squared	1.02955	3876	Low confidence	44613.5	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1	67.7402	Rooted	1.06647	767	High confidence	63.5181	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1	76.8115	Rooted	1.03323	2644	Low confidence	74.3411	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1	192.92	Ranked	1.01888	2252	Low confidence	196.562	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1	199.266	Ranked	1.03195	1025	High confidence	205.632	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1	6222.04	Measured	1.13536	563	High confidence	5480.24	
3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	1	8689.87	Measured	1.03137	2218	Low confidence	8425.53	

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/