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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

Results: HTML CSV LaTeX

Showing element 475 to 524 of 3228 in total

Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [source:swissprot;acc:q9uqm7]	1385	6079.45	6555.4	1.07829	
calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [source:swissprot;acc:q13554]	1386	6079.46	6555.41	1.07829	
calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	1376	6079.46	6555.41	1.07829	
calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	1375	6079.45	6555.4	1.07829	
calcyphosine. [source:swissprot;acc:q13938]	365	5189	6088.47	1.17334	
calmegin precursor. [source:swissprot;acc:o14967]	1473	5910.06	6355.08	1.0753	
calmodulin. [source:swissprot;acc:p02593]	2928	0.00001	0.00001	1	
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [source:swissprot;acc:p27824]	1474	5910.06	6355.08	1.0753	
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [source:swissprot;acc:p07384]	2384	4164.96	4336.92	1.04129	
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [source:swissprot;acc:p17655]	2383	4164.76	4337.01	1.04136	
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [source:swissprot;acc:p27797]	1526	5369.1	5763.72	1.0735	
calsyntenin-1 precursor. [source:swissprot;acc:o94985]	536	10603.5	12069.5	1.13826	
calsyntenin-2 precursor. [source:swissprot;acc:q9h4d0]	541	10600.3	12065.2	1.13819	
calsyntenin-3 precursor. [source:swissprot;acc:q9bqt9]	543	10599.9	12064.7	1.13819	
camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	1439	5658.8	6093.56	1.07683	
camp responsive element binding protein-like 2. [source:refseq;acc:nm_001310]	3078	0.00001	0.00001	1	
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [source:swissprot;acc:p10644]	3089	0.00001	0.00001	1	
camp-dependent protein kinase type ii-alpha regulatory chain. [source:swissprot;acc:p13861]	1710	5916.13	6321.77	1.06857	
camp-dependent protein kinase type ii-beta regulatory chain. [source:swissprot;acc:p31323]	1715	5918.48	6323.83	1.06849	
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [source:swissprot;acc:p17612]	1714	5917.23	6322.73	1.06853	
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [source:swissprot;acc:p22694]	1713	5917.23	6322.73	1.06853	
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [source:swissprot;acc:p22612]	1712	5917.23	6322.73	1.06853	
candidate tumor suppressor in ovarian cancer 2. [source:refseq;acc:nm_080822]	2025	4813.13	5091.36	1.05781	
carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	2351	8353.97	8001.45	1.04406	
carboxypeptidase a5. [source:refseq;acc:nm_080385]	2344	8353.97	8001.45	1.04406	
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	2345	8353.97	8001.45	1.04406	
carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	239	7711.38	6265.8	1.23071	
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [source:swissprot;acc:p16870]	719	6593.17	7364.55	1.117	
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [source:swissprot;acc:p15169]	717	6593.17	7364.55	1.117	
carcinoma related gene. [source:refseq;acc:nm_016041]	3179	0.00001	0.00001	1	
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [source:swissprot;acc:p43155]	1093	5791.05	6316.61	1.09075	
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [source:swissprot;acc:p23786]	2885	0.00001	0.00001	1	
cartilage oligomeric matrix protein precursor (comp). [source:swissprot;acc:p49747]	2220	3936.2	3755.33	1.04816	
casein kinase i alpha s-like. [source:refseq;acc:nm_145203]	953	4906.33	5382.5	1.09705	
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [source:swissprot;acc:p48729]	954	4906.33	5382.5	1.09705	
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [source:swissprot;acc:p48730]	1035	5054.73	5530.23	1.09407	
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [source:swissprot;acc:p49674]	1030	5048.33	5523.85	1.09419	
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [source:swissprot;acc:q9hcp0]	2830	0.00001	0.00001	1	
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [source:swissprot;acc:p78368]	2986	0.00001	0.00001	1	
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [source:swissprot;acc:q9y6m4]	2901	0.00001	0.00001	1	
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [source:swissprot;acc:p13862]	1245	4835.55	5243.23	1.08431	
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19138]	851	4307.12	4755.03	1.10399	
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [source:swissprot;acc:p19784]	852	4307.12	4755.03	1.10399	
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [source:swissprot;acc:p55210]	948	4633.48	5084.24	1.09728	
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	616	11222.2	9948.93	1.12798	
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	914	6513.45	7161	1.09942	
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [source:swissprot;acc:p07711]	2238	5902.27	6181.21	1.04726	
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [source:swissprot;acc:o60911]	2237	5902.26	6181.21	1.04726	
caveolin-1. [source:swissprot;acc:q03135]	3099	0.00001	0.00001	1	
caveolin-3 (m-caveolin). [source:swissprot;acc:p56539]	2779	0.00001	0.00001	1	

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/