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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 38536 in total

Filtered	0
Network Comparison Type	Divided

description	green	Value Type	network_comparison	Rank	Interaction Map	red	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	17.0804	Rooted	1.04801	537	Low confidence	16.298	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	18.0183	Rooted	1.5213	53	High confidence	11.844	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	851.77	Measured	1.31954	131	Low confidence	645.504	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	934.348	Measured	2.79409	37	High confidence	334.401	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	1034.13	Squared	10.2338	37	High confidence	101.05	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	1268.51	Squared	1.63527	146	Low confidence	775.72	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	13590.3	Ranked	1.02915	629	Low confidence	13205.3	
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	13895.8	Ranked	1.09822	242	High confidence	15260.6	
17-beta-hydroxysteroid dehydrogenase type vii-like. [source:refseq;acc:nm_182829]	39.5126	Rooted	1.0106	768	Low confidence	39.0982	
17-beta-hydroxysteroid dehydrogenase type vii-like. [source:refseq;acc:nm_182829]	4869.42	Measured	1.00902	778	Low confidence	4825.89	
17-beta-hydroxysteroid dehydrogenase type vii-like. [source:refseq;acc:nm_182829]	10050.9	Ranked	1.02953	627	Low confidence	10347.7	
17-beta-hydroxysteroid dehydrogenase type vii-like. [source:refseq;acc:nm_182829]	40451	Squared	1.00447	815	Low confidence	40270.8	
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	128.828	26	High confidence	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]	3.80565	Rooted	3.62106	26	High confidence	13.7805	
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]	9.42485	Rooted	1.20585	131	Low confidence	11.365	
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	11.6763	19	High confidence	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]	181.734	Measured	1.22585	171	Low confidence	222.779	
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]	296.481	Squared	1.03806	697	Low confidence	307.765	
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]	14695.2	Ranked	1.08587	384	Low confidence	13533.1	
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	1.42943	47	High confidence	12941.7	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	23.2445	Rooted	1.00582	793	Low confidence	23.11	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	32.0298	Rooted	1.04188	370	High confidence	30.7424	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	1609.88	Measured	1.01017	771	Low confidence	1593.68	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	2642.79	Measured	1.01545	451	High confidence	2683.61	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	6490.54	Squared	1.01738	763	Low confidence	6603.33	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	7355.46	Squared	1.17196	316	High confidence	8620.27	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	10806	Ranked	1.03909	379	High confidence	11228.4	
26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	11854.2	Ranked	1.00181	825	Low confidence	11832.8	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	26.5693	Rooted	1.01548	728	Low confidence	26.1642	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	28.5146	Rooted	1.01531	458	High confidence	28.0847	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	2263.85	Measured	1.00763	474	High confidence	2281.12	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	2331.31	Measured	1.00797	785	Low confidence	2349.9	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	5878.56	Squared	1.14785	328	High confidence	6747.71	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	11538	Ranked	1.02285	665	Low confidence	11801.6	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	11748.1	Ranked	1.00195	495	High confidence	11725.2	
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]	14694	Squared	1.07533	591	Low confidence	15800.9	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	44.9836	Rooted	1.025	438	High confidence	43.8864	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	44.9836	Rooted	1.025	662	Low confidence	43.8864	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	5046.33	Measured	1.00159	492	High confidence	5038.33	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	5046.33	Measured	1.00159	822	Low confidence	5038.33	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	11512.3	Ranked	1.07178	299	High confidence	12338.7	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	11512.3	Ranked	1.07178	453	Low confidence	12338.7	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	17901.1	Squared	1	493	High confidence	17901.1	
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]	17901.1	Squared	1	836	Low confidence	17901.1	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	25.4539	Rooted	1.06963	442	Low confidence	27.2263	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	31.1453	Rooted	1.03923	376	High confidence	32.3671	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	1932.95	Measured	1.04278	581	Low confidence	2015.65	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	2853.65	Measured	1.0252	438	High confidence	2925.57	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	10466.5	Ranked	1.05751	327	High confidence	9897.29	
3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	10485.1	Squared	1.03494	703	Low confidence	10851.4	

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/