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 6108 to 6157 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1527 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
1536 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Squared 31846.9 35454 1.11326
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Ranked 228.419 232.376 1.01732
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] Rooted 63.3039 65.6156 1.03652
1537 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] Squared 26432.8 29419.4 1.11299
evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581] Measured 6184.27 6637.44 1.07328
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] Rooted 63.3039 65.6156 1.03652
ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] Ranked 228.419 232.376 1.01732
1538 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Squared 30653.9 34111.1 1.11278
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] Rooted 63.304 65.6156 1.03652
elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] Ranked 228.419 232.376 1.01732
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Measured 5870.72 6300.83 1.07326
1539 26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] 5783.97 6207.5 1.07322
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] Rooted 63.304 65.6156 1.03652
colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Squared 29291.1 32591.4 1.11267
rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] Ranked 228.419 232.376 1.01732
1540 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 240.077 236.015 1.01721

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/