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 451 to 500 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
bup protein. [refseq;acc:nm_012071] 2911 0.00001 0.00001 1
bystin. [swissprot;acc:q13895] 1149 239.505 233.185 1.0271
c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 1766 228.932 231.732 1.01223
c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 2473 218.644 217.991 1.003
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1554 196.215 193.018 1.01656
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1558 196.171 192.977 1.01655
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 844 178.033 170.82 1.04223
c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 2475 218.219 217.571 1.00298
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 1625 217.446 214.2 1.01515
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 1506 212.103 208.339 1.01807
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 321 241.892 265.959 1.09949
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 260 219.421 196.978 1.11394
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 2577 192.625 192.922 1.00154
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 1448 226.532 222.117 1.01988
cab2. [refseq;acc:nm_033419] 769 210.946 221.225 1.04873
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 212.884 215.323 1.01146
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1526 219.306 223.179 1.01766
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1330 218.508 213.648 1.02275
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 218.509 213.649
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 194.527 195.08 1.00284
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] 940 212.442 205.088 1.03586
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 209.052 203.183 1.02889
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 215.925 214.481 1.00673
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] 563 220.744 207.121 1.06577
calmegin precursor. [swissprot;acc:o14967] 1909 217.48 215.256 1.01033
calmodulin. [swissprot;acc:p02593] 2928 0.00001 0.00001 1
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1910 217.48 215.256 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] 299 268.635 243.592 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] 298 268.632 243.588
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2181 227.117 225.62 1.00664
calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 188.435 188.31 1.00066
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 188.457 188.334 1.00065
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 188.459 188.336
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1363 218.591 213.899 1.02194
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 0.00001 0.00001 1
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 215.554 214.467 1.00507
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2313 215.529 214.449 1.00504
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 2312 215.542 214.459 1.00505
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] 2309
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 1173 229.243 235.246 1.02619
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 1422 203.979 208.229 1.02084
carboxypeptidase a5. [refseq;acc:nm_080385] 1417
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 1418

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/