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 6091 to 6140 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1523 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
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Squared 28606.2 31850.3 1.11341
1529 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Ranked 216.762 213.031 1.01751
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] Rooted 63.304 65.6156 1.03652
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Measured 5916.05 6350.53 1.07344
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] Squared 28606.2 31850.3 1.11341
1530 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Measured 5916.05 6350.53 1.07344
af-6 protein. [swissprot;acc:p55196] Ranked 218.733 214.98 1.01746
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Rooted 63.304 65.6156 1.03652
ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] Squared 28606.2 31850.3 1.11341
1531 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]
cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Ranked 217.025 213.304 1.01744
dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Measured 5916.05 6350.53 1.07344
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Rooted 63.3039 65.6156 1.03652
1532 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Measured 5916.05 6350.53 1.07344
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] Squared 28606.2 31850.3 1.11341
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] Rooted 63.304 65.6156 1.03652
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Ranked 228.419 232.376 1.01732
1533 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Measured 5916.05 6350.53 1.07344
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Rooted 63.304 65.6156 1.03652
cytochrome c. [swissprot;acc:p00001] Ranked 228.419 232.376 1.01732
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Squared 28606.2 31850.3 1.11341
1534 adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Measured 5916.05 6350.53 1.07344
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Rooted 63.304 65.6156 1.03652
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Ranked 228.419 232.376 1.01732
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Squared 28603.7 31846.4 1.11337
1535 heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Ranked 228.419 232.376 1.01732
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Rooted 63.304 65.6156 1.03652
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Squared 25840.7 28767.8 1.11327
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Measured 5916.05 6350.53 1.07344

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/