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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6062 to 6111 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1516 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Ranked 213.267 209.511 1.01793
lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055] Measured 5633.67 6050.69 1.07402
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Squared 21282.4 23701.9 1.11369
1517 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] Measured 5996.14 6439.46 1.07393
rho interacting protein 3. [refseq;acc:nm_015134] Squared 24157.2 26903.5 1.11368
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Ranked 213.267 209.511 1.01793
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Rooted 61.9527 64.2401 1.03692
1518 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Measured 10341.2 9630.35 1.07381
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Rooted 62.4888 64.793 1.03687
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Squared 24156 26902 1.11368
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Ranked 213.259 209.524 1.01783
1519 cone-rod homeobox protein. [swissprot;acc:o43186] 244.331 240.061 1.01779
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Measured 5283.8 5673.81 1.07381
mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Squared 28609.1 31855 1.11346
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Rooted 63.2569 65.5867 1.03683
1520 gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Measured 5283.8 5673.81 1.07381
homeobox protein otx1. [swissprot;acc:p32242] Ranked 244.367 240.098 1.01778
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Squared 28606.2 31850.3 1.11341
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Rooted 63.2569 65.5867 1.03683
1521 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] Measured 5938.56 6376.76 1.07379
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] Squared 28606.2 31850.3 1.11341
homeobox protein otx2. [swissprot;acc:p32243] Ranked 244.478 240.212 1.01776
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Rooted 63.2569 65.5867 1.03683
1522 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] Squared 28606.2 31850.3 1.11341
glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] Measured 6137.24 6589.72 1.07373
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Ranked 219.306 223.179 1.01766
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Rooted 62.1861 64.4641 1.03663
1523 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] Measured 6137.09 6589.57 1.07373
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Squared 28606.2 31850.3 1.11341
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Ranked 219.306 223.179 1.01766
regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Rooted 61.2323 63.4727 1.03659
1524 glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] Measured 6137.53 6590.01 1.07372
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Ranked 219.306 223.179 1.01766
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Rooted 62.1787 64.4541 1.03659
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Squared 28606.2 31850.3 1.11341
1525 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Rooted 63.306 65.619 1.03654
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Ranked 219.306 223.179 1.01766
ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] Squared 28606.2 31850.3 1.11341
tensin. [refseq;acc:nm_022648] Measured 5871.89 6303.56 1.07351
1526 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Squared 28606.2 31850.3 1.11341
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Ranked 219.306 223.179 1.01766
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] Measured 5369.1 5763.72 1.0735
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Rooted 63.3039 65.6156 1.03652
1527 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] Measured 5926.76 6362.33 1.07349
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Squared 28606.2 31850.3 1.11341
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Ranked 219.306 223.179 1.01766
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Rooted 64.0491 66.3884 1.03652
1528 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] Measured 5869.97 6301.24 1.07347
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] Rooted 63.304 65.6156 1.03652
hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] Ranked 217.785 214.021 1.01759

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/