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 3358 to 3407 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
420 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Squared Subtracted 32192.8 37967.1 5774.3
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured Divided 10235.2 11830.8 1.15589
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Subtracted 5942.49 6853.15 910.66
421 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted Divided 50.4666 45.9317 1.09873
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Squared 36933 44953.6 1.21717
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Measured Subtracted 6739.43 7644.55 905.12
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Squared 32189.9 37963.6 5773.7
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Ranked 238.704 255.68 16.976
thrombospondin 3 precursor. [swissprot;acc:p49746] Rooted 51.6132 45.8422 5.771
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Ranked Divided 223.202 205.9 1.08403
vav-2 protein. [swissprot;acc:p52735] Measured 6660.02 7697.78 1.15582
422 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted 50.4641 45.9293 1.09873
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured Subtracted 460 1365 905
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Squared Divided 25860 31475.4 1.21715
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 32188.2 37961.6 5773.4
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured Divided 5206.9 6010.04 1.15425
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted Subtracted 80.4069 86.1018 5.6949
ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked Divided 240.287 260.193 1.08284
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Subtracted 238.704 255.68 16.976
423 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Rooted Divided 50.4663 45.9313 1.09873
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Measured Subtracted 6739.61 7644.58 904.97
Squared 32187.7 37961 5773.3
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Rooted 60.0148 65.6429 5.6281
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Measured Divided 5207.03 6010.1 1.15423
oligophrenin 1. [swissprot;acc:o60890] Ranked Subtracted 238.704 255.68 16.976
ras-related protein rab-26. [swissprot;acc:q9ulw5] Divided 240.287 260.193 1.08284
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Squared 36735.7 44689.6 1.21652
424 60s ribosomal protein l23a. [swissprot;acc:p29316] Rooted 50.4703 45.9373 1.09868
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 1.08284
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Squared Subtracted 32183.5 37955.7 5772.2
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Measured 6739.63 7644.59 904.96
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Rooted 51.9812 57.5858 5.6046
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Squared Divided 20259.5 24635.7 1.21601
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Measured 5207.78 6010.45 1.15413
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Ranked Subtracted 251.83 234.951 16.879
425 40s ribosomal protein s20. [swissprot;acc:p17075] Rooted Divided 50.0161 45.5318 1.09849
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked Subtracted 212.547 229.411 16.864
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Measured 6739.7 7644.6 904.9
max protein. [swissprot;acc:p25912] Ranked Divided 227.828 210.561 1.082
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Squared 20258.6 24634.7 1.21601
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Rooted Subtracted 48.1584 53.7378 5.5794
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Measured Divided 3729.02 4301.58 1.15354
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Squared Subtracted 28408.7 34148.5 5739.8
426 dendritic cell protein. [refseq;acc:nm_006360] 33104 38818.5 5714.5
dynactin 4. [refseq;acc:nm_032486] Ranked Divided 233.142 252.253 1.08197
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Measured Subtracted 6739.81 7644.62 904.81
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Rooted 66.0815 71.6562 5.5747
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Divided 55.1073 60.5285 1.09838
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Measured 5942.49 6853.15 1.15325
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked Subtracted 212.547 229.411 16.864

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/