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