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 Value Type Gene green Interaction Map Network Comparison Type Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 3228 in total
Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
green
red
network_comparison
bup protein. [refseq;acc:nm_012071] 2911 0.00001 0.00001 1
bystin. [swissprot;acc:q13895] 950 4697.02 4280.99 1.09718
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] 2102 5127.3 4860.34 1.05493
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] 1962 6297.78 5941.24 1.06001
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1638 9248.18 9895.77 1.07002
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1630 9253.79 9903.22 1.07018
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 488 12447 10872.4 1.14483
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] 1528 6301.24 5869.97 1.07347
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 707 5944.25 5317.78 1.11781
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 2120 7329 6951.29 1.05434
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 2174 3463.02 3641.45 1.05152
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 2421 7088.93 7355.46 1.0376
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 874 10941.2 9921.43 1.10278
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] 941 5455.34 4970.21 1.09761
cab2. [refseq;acc:nm_033419] 2618 5683 5599.85 1.01485
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] 1217 6536.45 6021.21 1.08557
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1723 5830.76 5458.12 1.06827
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1356 6103.57 5657.71 1.07881
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] 1360 6103.52 5657.72 1.07879
calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] 1361
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] 1913 7287.27 6858.84 1.06246
calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] 1916
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 440 7192.08 6251.91 1.15038
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] 606 6955.76 6148.94 1.13121
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] 1385 6555.4 6079.45 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). [swissprot;acc:q13554] 1386 6555.41 6079.46
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] 1376
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] 1375 6555.4 6079.45
calcyphosine. [swissprot;acc:q13938] 365 6088.47 5189 1.17334
calmegin precursor. [swissprot;acc:o14967] 1473 6355.08 5910.06 1.0753
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] 1474 6355.08 5910.06 1.0753
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 2384 4336.92 4164.96 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). [swissprot;acc:p17655] 2383 4337.01 4164.76 1.04136
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 1526 5763.72 5369.1 1.0735
calsyntenin-1 precursor. [swissprot;acc:o94985] 536 12069.5 10603.5 1.13826
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 541 12065.2 10600.3 1.13819
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 543 12064.7 10599.9
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1439 6093.56 5658.8 1.07683
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] 1710 6321.77 5916.13 1.06857
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 1715 6323.83 5918.48 1.06849
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 1714 6322.73 5917.23 1.06853
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 1713
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 1712
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 2025 5091.36 4813.13 1.05781
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 2351 8001.45 8353.97 1.04406
carboxypeptidase a5. [refseq;acc:nm_080385] 2344
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 2345

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/