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