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 Gene Interaction Map red network_comparison Network Comparison Type

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Showing element 1 to 50 of 14920 in total

Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

description	green	Value Type	Rank	red	network_comparison	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	18.0183	Rooted	53	11.844	1.5213	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	934.348	Measured	37	334.401	2.79409	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	1034.13	Squared	37	101.05	10.2338	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	13895.8	Ranked	242	15260.6	1.09822	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	0.344399	Squared	26	44.3683	128.828	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	3.80565	Rooted	26	13.7805	3.62106	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	26.1599	Measured	19	305.45	11.6763	
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	18499.2	Ranked	47	12941.7	1.42943	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	32.0298	Rooted	370	30.7424	1.04188	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	2642.79	Measured	451	2683.61	1.01545	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	7355.46	Squared	316	8620.27	1.17196	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	10806	Ranked	379	11228.4	1.03909	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	28.5146	Rooted	458	28.0847	1.01531	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	2263.85	Measured	474	2281.12	1.00763	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	5878.56	Squared	328	6747.71	1.14785	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	11748.1	Ranked	495	11725.2	1.00195	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	44.9836	Rooted	438	43.8864	1.025	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	5046.33	Measured	492	5038.33	1.00159	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	11512.3	Ranked	299	12338.7	1.07178	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	17901.1	Squared	493	17901.1	1	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	31.1453	Rooted	376	32.3671	1.03923	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	2853.65	Measured	438	2925.57	1.0252	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	10466.5	Ranked	327	9897.29	1.05751	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	18218.3	Squared	477	18353.1	1.0074	
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]	26.8141	Rooted	357	28.0711	1.04688	
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]	1721.76	Measured	346	1837.26	1.06708	
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]	6794.39	Squared	455	6970.13	1.02587	
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]	10243.1	Ranked	478	10156.4	1.00854	
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	0.145878	Squared	232	0.108639	1.34278	
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	2.18581	Rooted	36	4.30525	1.96964	
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	14.3333	Measured	121	19.6667	1.3721	
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	19704.7	Ranked	369	18849.7	1.04536	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	23.5833	Rooted	251	21.3142	1.10646	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	1337.54	Measured	258	1183.16	1.13048	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	3201.81	Squared	270	2569.37	1.24615	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	11013.2	Ranked	222	12183	1.10622	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	26.17	Rooted	225	23.1768	1.12915	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	1735.23	Measured	222	1499.4	1.15728	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	6172.1	Squared	241	4734.34	1.30369	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	10592.8	Ranked	186	11935.1	1.12672	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	5.24885	Squared	152	8.80383	1.67729	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	5.66499	Rooted	43	9.92134	1.75134	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	81.2233	Measured	58	150.741	1.85588	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	17098	Ranked	112	14269.7	1.1982	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	30.9731	Rooted	395	32.0326	1.03421	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	2378.99	Measured	444	2431.87	1.02223	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	6524	Squared	472	6605.9	1.01255	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	9936.37	Ranked	380	9566.15	1.0387	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	12.5026	Rooted	285	13.5612	1.08467	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	405.367	Measured	385	387.486	1.04615	

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/