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.


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 [...,...].
Gene description Rank Value Type Filtered Network Comparison Type network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 551 to 600 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
network_comparison
green
red
cab2. [refseq;acc:nm_033419] 7 0 1.99689 10950 21866
769 1 1.04873 221.225 210.946
cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 1829 1.01146 215.323 212.884
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1526 1.01766 223.179 219.306
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1330 1.02275 213.648 218.508
calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] 1328 213.649 218.509
calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] 1331
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] 2494 1.00284 195.08 194.527
calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] 2497
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 940 1.03586 205.088 212.442
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 1100 1.02889 203.183 209.052
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). [swissprot;acc:q9uqm7] 2172 1.00673 214.481 215.925
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] 2173
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] 2162
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] 2161
calcyphosine. [swissprot;acc:q13938] 374 0 1.04183 9478.1 9874.54
563 1 1.06577 207.121 220.744
calmegin precursor. [swissprot;acc:o14967] 1909 1.01033 215.256 217.48
calmodulin. [swissprot;acc:p02593] 2928 1 0.00001 0.00001
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1910 1.01033 215.256 217.48
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 299 1.10281 243.592 268.635
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] 298 243.588 268.632
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2181 1.00664 225.62 227.117
calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 1.00066 188.31 188.435
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 1.00065 188.334 188.457
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 188.336 188.459
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1363 1.02194 213.899 218.591
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 1 0.00001 0.00001
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089
camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 2307 1.00507 214.467 215.554
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2313 1.00504 214.449 215.529
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 2312 1.00505 214.459 215.542
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 2311
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 300 0 1.0717 8650.24 9270.49
2309 1 1.00505 214.459 215.542
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 1173 1.02619 235.246 229.243
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 1422 1.02084 208.229 203.979
carboxypeptidase a5. [refseq;acc:nm_080385] 1417
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 1418
carboxypeptidase b precursor. [refseq;acc:nm_020361] 509 1.07057 190.239 177.698
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 347 0 1.0491 7311 7670
717 1 1.05402 211.685 223.121
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 715
carcinoma related gene. [refseq;acc:nm_016041] 3179 1 0.00001 0.00001
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 1698 1.01367 214.69 217.624
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 2885 1 0.00001 0.00001
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 50 0 1.41533 13091.4 9249.73
226 1 1.12187 269.238 239.991
casein kinase i alpha s-like. [refseq;acc:nm_145203] 343 0 1.05173 8788.62 8356.31
1495 1 1.01874 225.237 229.459

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/