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 green Rank Gene Interaction Map Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 14920 in total 
Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

description	Value Type	green	Rank	red	network_comparison	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Measured	934.348	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]	Ranked	13895.8	242	15260.6	1.09822	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Squared	1034.13	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]	Rooted	18.0183	53	11.844	1.5213	
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	26.1599	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]	Ranked	18499.2	47	12941.7	1.42943	
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	0.344399	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]	Rooted	3.80565	26	13.7805	3.62106	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Measured	2642.79	451	2683.61	1.01545	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Ranked	10806	379	11228.4	1.03909	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Squared	7355.46	316	8620.27	1.17196	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Rooted	32.0298	370	30.7424	1.04188	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Measured	2263.85	474	2281.12	1.00763	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Ranked	11748.1	495	11725.2	1.00195	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Squared	5878.56	328	6747.71	1.14785	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	Rooted	28.5146	458	28.0847	1.01531	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Measured	5046.33	492	5038.33	1.00159	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Ranked	11512.3	299	12338.7	1.07178	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Squared	17901.1	493	17901.1	1	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	Rooted	44.9836	438	43.8864	1.025	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Measured	2853.65	438	2925.57	1.0252	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Ranked	10466.5	327	9897.29	1.05751	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Squared	18218.3	477	18353.1	1.0074	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	Rooted	31.1453	376	32.3671	1.03923	
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	1721.76	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]	Ranked	10243.1	478	10156.4	1.00854	
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	6794.39	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]	Rooted	26.8141	357	28.0711	1.04688	
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	14.3333	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]	Ranked	19704.7	369	18849.7	1.04536	
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	0.145878	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]	Rooted	2.18581	36	4.30525	1.96964	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Measured	1337.54	258	1183.16	1.13048	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Ranked	11013.2	222	12183	1.10622	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Squared	3201.81	270	2569.37	1.24615	
40s ribosomal protein s15 (rig protein). [source:swissprot;acc:p11174]	Rooted	23.5833	251	21.3142	1.10646	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Measured	1735.23	222	1499.4	1.15728	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Ranked	10592.8	186	11935.1	1.12672	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Squared	6172.1	241	4734.34	1.30369	
40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Rooted	26.17	225	23.1768	1.12915	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Measured	81.2233	58	150.741	1.85588	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Ranked	17098	112	14269.7	1.1982	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Squared	5.24885	152	8.80383	1.67729	
40s ribosomal protein s26. [source:swissprot;acc:p02383]	Rooted	5.66499	43	9.92134	1.75134	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Measured	2378.99	444	2431.87	1.02223	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Ranked	9936.37	380	9566.15	1.0387	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Squared	6524	472	6605.9	1.01255	
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [source:swissprot;acc:p42677]	Rooted	30.9731	395	32.0326	1.03421	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Measured	405.367	385	387.486	1.04615	
40s ribosomal protein s28. [source:swissprot;acc:p25112]	Ranked	14193.6	258	12967.1	1.09459	

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/