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 Interaction Map Network Comparison Type Filtered red network_comparison green
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
red
network_comparison
green
bup protein. [refseq;acc:nm_012071] 2911 0.00001 1 0.00001
bystin. [swissprot;acc:q13895] 950 4280.99 1.09718 4697.02
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 4860.34 1.05493 5127.3
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 5941.24 1.06001 6297.78
c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1638 9895.77 1.07002 9248.18
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1630 9903.22 1.07018 9253.79
c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 488 10872.4 1.14483 12447
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 5869.97 1.07347 6301.24
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 707 5317.78 1.11781 5944.25
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 2120 6951.29 1.05434 7329
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 2174 3641.45 1.05152 3463.02
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 2421 7355.46 1.0376 7088.93
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 874 9921.43 1.10278 10941.2
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 4970.21 1.09761 5455.34
cab2. [refseq;acc:nm_033419] 2618 5599.85 1.01485 5683
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 6021.21 1.08557 6536.45
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1723 5458.12 1.06827 5830.76
calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1356 5657.71 1.07881 6103.57
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 5657.72 1.07879 6103.52
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 6858.84 1.06246 7287.27
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 6251.91 1.15038 7192.08
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 6148.94 1.13121 6955.76
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 6079.45 1.07829 6555.4
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 6079.46 6555.41
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 6079.45 6555.4
calcyphosine. [swissprot;acc:q13938] 365 5189 1.17334 6088.47
calmegin precursor. [swissprot;acc:o14967] 1473 5910.06 1.0753 6355.08
calmodulin. [swissprot;acc:p02593] 2928 0.00001 1 0.00001
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1474 5910.06 1.0753 6355.08
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 2384 4164.96 1.04129 4336.92
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 4164.76 1.04136 4337.01
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 1526 5369.1 1.0735 5763.72
calsyntenin-1 precursor. [swissprot;acc:o94985] 536 10603.5 1.13826 12069.5
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 541 10600.3 1.13819 12065.2
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 543 10599.9 12064.7
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1439 5658.8 1.07683 6093.56
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 0.00001 1 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] 1710 5916.13 1.06857 6321.77
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 1715 5918.48 1.06849 6323.83
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 1714 5917.23 1.06853 6322.73
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 4813.13 1.05781 5091.36
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 2351 8353.97 1.04406 8001.45
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/