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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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
description
Rank
Network Comparison Type
red
green
network_comparison
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). [swissprot;acc:q13554] 2149 Subtracted 215.925 214.481 1.444
2173 Divided 1.00673
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). [swissprot;acc:q13557] 2139 Subtracted 1.444
2162 Divided 1.00673
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). [swissprot;acc:q13555] 2138 Subtracted 1.444
2161 Divided 1.00673
calcyphosine. [swissprot;acc:q13938] 563 220.744 207.121 1.06577
565 Subtracted 13.623
calmegin precursor. [swissprot;acc:o14967] 1880 217.48 215.256 2.224
1909 Divided 1.01033
calmodulin. [swissprot;acc:p02593] 2928 0.00001 0.00001 1
Subtracted 0 0 0
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1881 217.48 215.256 2.224
1910 Divided 1.01033
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 205 Subtracted 268.635 243.592 25.043
299 Divided 1.10281
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). [swissprot;acc:p17655] 204 Subtracted 268.632 243.588 25.044
298 Divided 1.10281
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2124 Subtracted 227.117 225.62 1.497
2181 Divided 1.00664
calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 188.435 188.31 1.00066
2707 Subtracted 0.125
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 Divided 188.457 188.334 1.00065
2713 Subtracted 0.123
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 Divided 188.459 188.336 1.00065
2714 Subtracted 0.123
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1318 218.591 213.899 4.692
1363 Divided 1.02194
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 0.00001 0.00001 1
Subtracted 0 0 0
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089 Divided 0.00001 0.00001 1
Subtracted 0 0 0
camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 2292 215.554 214.467 1.087
2307 Divided 1.00507
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2297 Subtracted 215.529 214.449 1.08
2313 Divided 1.00504
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 2296 Subtracted 215.542 214.459 1.083
2312 Divided 1.00505
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 2295 Subtracted 1.083
2311 Divided 1.00505
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 2294 Subtracted 1.083
2309 Divided 1.00505
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 1069 Subtracted 229.243 235.246 6.003
1173 Divided 1.02619
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 1422 203.979 208.229 1.02084
1425 Subtracted 4.25
carboxypeptidase a5. [refseq;acc:nm_080385] 1417 Divided 1.02084
1421 Subtracted 4.25
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 1418 Divided 1.02084
1422 Subtracted 4.25

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/