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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Value Type Interaction Map description Rank Network Comparison Type Gene red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 294 to 343 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [source:swissprot;acc:p42574]	949	4633.48	5084.24	1.09728	
apoptosis antagonizing transcription factor. [source:refseq;acc:nm_012138]	853	4078.45	4502.32	1.10393	
apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	771	5874.74	6533.34	1.11211	
apoptosis inhibitor fksg2. [source:swissprot;acc:q9hau6]	2589	7181.3	7057.99	1.01747	
apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [source:refseq;acc:nm_032797]	1496	5945.56	6389.63	1.07469	
apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [source:refseq;acc:nm_014481]	1225	5546.5	6019.57	1.08529	
aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	523	10640.2	12117.8	1.13887	
aquaporin 5. [source:swissprot;acc:p55064]	524	10640	12117.6	1.13887	
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [source:swissprot;acc:p41181]	526	10639.9	12117.4	1.13886	
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [source:swissprot;acc:p29972]	528	10635.3	12111.4	1.13879	
arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [source:swissprot;acc:q9y2x7]	2219	5853.67	6136.97	1.0484	
arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [source:swissprot;acc:q14161]	2252	5840.54	6113.01	1.04665	
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	436	6230.94	7168.2	1.15042	
arginase 1 (ec 3.5.3.1) (liver-type arginase). [source:swissprot;acc:p05089]	1852	6271.17	6670.97	1.06375	
arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [source:swissprot;acc:p78540]	1849	6267.93	6668.72	1.06394	
arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	2278	5783.76	6048.94	1.04585	
arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [source:swissprot;acc:q15815]	993	6499.89	7121.77	1.09568	
argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	1123	5857.48	6380.4	1.08927	
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [source:swissprot;acc:p00966]	1739	5695.57	6079.61	1.06743	
arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	839	7093.86	7842.67	1.10556	
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]	2798	0.00001	0.00001	1	
armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	698	7101.95	7949.85	1.11939	
arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [source:swissprot;acc:o15511]	1788	5386.49	5744.76	1.06651	
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [source:swissprot;acc:o15145]	1784	5386.37	5744.89	1.06656	
arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [source:swissprot;acc:o15144]	1750	5384.89	5746.51	1.06715	
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [source:swissprot;acc:o15143]	1781	5386.37	5744.89	1.06656	
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [source:swissprot;acc:o43681]	2525	8695.15	8912.98	1.02505	
aryl-hydrocarbon interacting protein-like 1. [source:swissprot;acc:q9nzn9]	1903	5204.25	5530.11	1.06261	
asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	1206	5946.33	6459.79	1.08635	
asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	730	6000.23	6696.89	1.11611	
asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [source:swissprot;acc:o43776]	2103	6847.82	7223.51	1.05486	
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	1010	5791.82	6340.86	1.0948	
aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [source:swissprot;acc:p14868]	2026	6766.45	7155.54	1.0575	
associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	146	11068	8508.5	1.30082	
associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	148	11068	8508.5	1.30082	
ataxin 2 related protein isoform a; ataxin-2 domain protein. [source:refseq;acc:nm_007245]	602	4864.66	5514.87	1.13366	
ataxin 2-binding protein. [source:swissprot;acc:q9nwb1]	2117	5778.16	6093.65	1.0546	
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [source:refseq;acc:nm_002973]	603	4864.66	5514.87	1.13366	
ataxin-1 ubiquitin-like interacting protein. [source:refseq;acc:nm_020131]	2645	9128.19	9218.44	1.00989	
atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	206	5720.25	4577.5	1.24965	
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p25705]	834	5623.18	6218.77	1.10592	
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	1970	4374.32	4126.96	1.05994	
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p06576]	869	5595.65	6173.23	1.10322	
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]	2893	0.00001	0.00001	1	
atp synthase coupling factor b, mitochondrial precursor. [source:swissprot;acc:q99766]	1507	6152.78	6610.46	1.07439	
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p30049]	811	6000.07	6655.11	1.10917	
atp synthase f chain, mitochondrial (ec 3.6.3.14). [source:swissprot;acc:p56134]	2036	6920.71	7315.59	1.05706	
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]	2834	0.00001	0.00001	1	
atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	824	5657.53	6263.02	1.10702	
atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691]	1657	5488.7	5131.89	1.06953	

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/