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 Value Type Gene Interaction Map description Network Comparison Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 25776 to 25825 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
green
red
network_comparison
2720 Rooted c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Subtracted 78.151 78.2186 0.0676
2721 Measured oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 3972.32 3953.53 18.79
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Divided 5583.64 5603.24 1.00351
Ranked bifunctional aminoacyl-trna synthetase [includes: glutamyl-trna synthetase (ec 6.1.1.17) (glutamate--trna ligase); prolyl-trna synthetase (ec 6.1.1.15) (proline--trna ligase)]. [swissprot;acc:p07814] 221.116 221.022 1.00043
Subtracted 0.094
Squared bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Divided 44464 45034.4 1.01283
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Subtracted 2366.62 2613.69 247.07
Rooted block 23. [sptrembl;acc:q8nhw5] Divided 58.4056 58.3407 1.00111
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Subtracted 67.4829 67.416 0.0669
2722 Measured alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920] Divided 5583.64 5603.24 1.00351
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Subtracted 3972.32 3953.53 18.79
Ranked transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Divided 219.214 219.308 1.00043
Subtracted 0.094
Squared guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] 2367 2614.02 247.02
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Divided 44464 45034.4 1.01283
Rooted glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Subtracted 67.4829 67.416 0.0669
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Divided 58.3966 58.3343 1.00107
2723 Measured adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] 5583.64 5603.24 1.00351
oligophrenin 1. [swissprot;acc:o60890] Subtracted 3972.32 3953.53 18.79
Ranked lamin b2. [swissprot;acc:q03252] Divided 219.413 219.323 1.00041
Subtracted 0.09
Squared guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] 2367 2614.02 247.02
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Divided 44464 45034.4 1.01283
Rooted succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 64.3084 64.3749 1.00103
Subtracted 0.0665
2724 Measured n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] 5351.72 5332.98 18.74
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Divided 5583.64 5603.24 1.00351
Ranked heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] 220.963 221.053 1.00041
Subtracted 0.09
Squared guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 2624.64 2834 209.36
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Divided 44464 45034.4 1.01283
Rooted dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Subtracted 72.603 72.5366 0.0664
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Divided 67.4829 67.416 1.00099
2725 Measured huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Subtracted 5351.72 5332.98 18.74
syntaxin 1b. [swissprot;acc:q15531] Divided 5583.64 5603.24 1.00351
Ranked doublecortin (lissencephalin-x) (lis-x) (doublin). [swissprot;acc:o43602] 216.569 216.496 1.00034
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] Subtracted 220.927 221.001 0.074
Squared germ cell-less. [refseq;acc:nm_022471] Divided 44461 45030.7 1.01281
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] Subtracted 33979.8 34173.9 194.1
Rooted glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Divided 67.4829 67.416 1.00099
helicase (fragment). [sptrembl;acc:q92771] Subtracted 72.6019 72.5359 0.066
2726 Measured fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Divided 5351.72 5332.98 1.00351
mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Subtracted 18.74
Ranked atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 220.927 221.001 0.074
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] Divided 1.00033
Squared adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] 29898.1 30233.2 1.01121
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Subtracted 33979.3 34173 193.7
Rooted b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 78.1394 78.2048 0.0654
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Divided 66.332 66.27 1.00094
2727 Measured fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Subtracted 5351.72 5332.98 18.74

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/