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 green Gene Interaction Map Network Comparison Type network_comparison red

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Showing element 1 to 50 of 14920 in total

Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

description	Value Type	Rank	green	network_comparison	red	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Measured	37	934.348	2.79409	334.401	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Ranked	242	13895.8	1.09822	15260.6	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Squared	37	1034.13	10.2338	101.05	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Rooted	53	18.0183	1.5213	11.844	
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]	Measured	19	26.1599	11.6763	305.45	
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]	Ranked	47	18499.2	1.42943	12941.7	
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]	Squared	26	0.344399	128.828	44.3683	
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]	Rooted	26	3.80565	3.62106	13.7805	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Measured	451	2642.79	1.01545	2683.61	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Ranked	379	10806	1.03909	11228.4	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Squared	316	7355.46	1.17196	8620.27	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Rooted	370	32.0298	1.04188	30.7424	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Measured	474	2263.85	1.00763	2281.12	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Ranked	495	11748.1	1.00195	11725.2	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Squared	328	5878.56	1.14785	6747.71	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Rooted	458	28.5146	1.01531	28.0847	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Measured	492	5046.33	1.00159	5038.33	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Ranked	299	11512.3	1.07178	12338.7	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Squared	493	17901.1	1	17901.1	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Rooted	438	44.9836	1.025	43.8864	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Measured	438	2853.65	1.0252	2925.57	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Ranked	327	10466.5	1.05751	9897.29	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Squared	477	18218.3	1.0074	18353.1	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Rooted	376	31.1453	1.03923	32.3671	
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]	Measured	346	1721.76	1.06708	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]	Ranked	478	10243.1	1.00854	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]	Squared	455	6794.39	1.02587	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]	Rooted	357	26.8141	1.04688	28.0711	
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]	Measured	121	14.3333	1.3721	19.6667	
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]	Ranked	369	19704.7	1.04536	18849.7	
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]	Squared	232	0.145878	1.34278	0.108639	
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]	Rooted	36	2.18581	1.96964	4.30525	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Measured	258	1337.54	1.13048	1183.16	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Ranked	222	11013.2	1.10622	12183	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Squared	270	3201.81	1.24615	2569.37	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Rooted	251	23.5833	1.10646	21.3142	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Measured	222	1735.23	1.15728	1499.4	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Ranked	186	10592.8	1.12672	11935.1	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Squared	241	6172.1	1.30369	4734.34	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Rooted	225	26.17	1.12915	23.1768	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Measured	58	81.2233	1.85588	150.741	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Ranked	112	17098	1.1982	14269.7	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Squared	152	5.24885	1.67729	8.80383	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Rooted	43	5.66499	1.75134	9.92134	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Measured	444	2378.99	1.02223	2431.87	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Ranked	380	9936.37	1.0387	9566.15	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Squared	472	6524	1.01255	6605.9	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Rooted	395	30.9731	1.03421	32.0326	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Measured	385	405.367	1.04615	387.486	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Ranked	258	14193.6	1.09459	12967.1	

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/