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 2100 to 2149 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1050 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Divided 4757.46 5198.91 1.09279
1051 homeobox protein dlx-2. [swissprot;acc:q07687]
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Subtracted 5208.27 5737.17 528.9
1052 homeobox protein dlx-5. [swissprot;acc:p56178] Divided 4757.46 5198.91 1.09279
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Subtracted 6278.76 6807.51 528.75
1053 fetal brain protein 239 (239fb). [swissprot;acc:q15777] Divided 4757.46 5198.91 1.09279
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 5166.04 5694.55 528.51
1054 heat shock factor binding protein 1. [swissprot;acc:o75506] 5915.42 6443.77 528.35
homeobox protein dlx-3. [swissprot;acc:o60479] Divided 4757.46 5198.91 1.09279
1055 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Subtracted 5167.15 5695.44 528.29
1056 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Divided 4757.46 5198.91 1.09279
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Subtracted 6413.32 6941.48 528.16
1057 mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] 5168.01 5696.12 528.11
tata element modulatory factor (tmf). [swissprot;acc:p82094] Divided 5412.23 5913.4 1.0926
1058 protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Subtracted 6275.86 6803.95 528.09
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Divided 5412.23 5913.4 1.0926
1059 tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Subtracted 3853.64 4379.71 526.07
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Divided 5719.01 6248.6 1.0926
1060 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Subtracted 5791.05 6316.61 525.56
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Divided 5719.01 6248.6 1.0926
1061 hskin17 protein. [refseq;acc:nm_012311] Subtracted 5791.05 6316.61 525.56
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Divided 5412.23 5913.4 1.0926
1062 ammecr1 protein. [refseq;acc:nm_015365]
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Subtracted 5791.05 6316.61 525.56
1063 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Divided 5412.23 5913.4 1.0926
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Subtracted 5791.05 6316.61 525.56
1064 dead-box protein. [refseq;acc:nm_018665] Divided 5719.01 6248.6 1.0926
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Subtracted 5791.05 6316.61 525.56
1065 dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 6350.81 6874.88 524.07
dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Divided 6393.81 6984.94 1.09245
1066 junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Subtracted 5732.73 6256.63 523.9
leucyl-trna synthetase. [refseq;acc:nm_020117] Divided 5417.06 5917.79 1.09244
1067 probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] 5417.07 1.09243
tax interaction protein 1. [refseq;acc:nm_014604] Subtracted 5732.73 6256.63 523.9
1068 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 5857.48 6380.4 522.92
exocyst complex component sec15a. [swissprot;acc:q8tag9] Divided 6201.54 6774.35 1.09237
1069 elongation factor 2 (ef-2). [swissprot;acc:p13639] 5494.73 6001.08 1.09215
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Subtracted 6251.32 6774.12 522.8
1070 metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Divided 5494.73 6001.08 1.09215
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Subtracted 6042.31 6565.03 522.72
1071 40s ribosomal protein s30. [swissprot;acc:q05472] 5893.97 6416.07 522.1
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Divided 5494.73 6001.08 1.09215
1072 electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Subtracted 7794.41 8316.04 521.63
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Divided 5207.39 5687.2 1.09214
1073 dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Subtracted 5364.3 5885.48 521.18
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Divided 5207.39 5687.2 1.09214
1074 putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Subtracted 5364.3 5885.48 521.18
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Divided 5207.39 5687.2 1.09214
1075 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Subtracted 4359.82 4880.99 521.17

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/