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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 4786 to 4835 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1197 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Measured 5721.19 6217.2 1.0867
mstp028 protein. [refseq;acc:nm_031954] Ranked 219.042 213.6 1.02548
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Squared 26914.1 30594.2 1.13674
1198 homeobox protein otx2. [swissprot;acc:p32243] Rooted 56.0239 58.6274 1.04647
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Squared 26914.1 30594.2 1.13674
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Ranked 269.59 276.454 1.02546
snare associated protein snapin. [refseq;acc:nm_012437] Measured 5721.19 6217.2 1.0867
1199 n-myc proto-oncogene protein. [swissprot;acc:p04198] Squared 20816.6 23663.1 1.13674
pxr2b protein. [refseq;acc:nm_016559] Rooted 66.7327 69.832 1.04644
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Measured 5449.48 5921.77 1.08667
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Ranked 241.496 235.508 1.02543
1200 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Squared 26914.1 30594.2 1.13674
homeobox protein otx1. [swissprot;acc:p32242] Rooted 56.0736 58.677 1.04643
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Ranked 219.03 213.604 1.0254
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Measured 5950.27 6465.72 1.08663
1201 cone-rod homeobox protein. [swissprot;acc:o43186] Rooted 56.0896 58.6931 1.04642
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Squared 19317.7 21958.6 1.13671
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Ranked 210.986 216.344 1.0254
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Measured 6042.31 6565.03 1.08651
1202 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] Ranked 227.274 233.041 1.02537
myb-related protein b (b-myb). [swissprot;acc:p10244] Rooted 60.1108 62.9002 1.0464
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Measured 4913.07 5337.95 1.08648
skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] Squared 19317.7 21958.6 1.13671
1203 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Measured 4322.65 4696.04 1.08638
myb-related protein a (a-myb). [swissprot;acc:p10243] Rooted 60.1161 62.9033 1.04636
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Ranked 219.023 213.606 1.02536
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Squared 19317.7 21958.6 1.13671
1204 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] Ranked 219.022 213.607 1.02535
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Rooted 63.2865 66.2117 1.04622
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Measured 5946.33 6459.79 1.08635
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Squared 19317.7 21958.6 1.13671
1205 glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Measured 5946.33 6459.79 1.08635
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Ranked 224.805 219.251 1.02533
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Rooted 64.7548 67.7419 1.04613
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Squared 19317.7 21958.6 1.13671
1206 asc-1 complex subunit p100. [refseq;acc:nm_032204] Measured 5946.33 6459.79 1.08635
integral membrane protein cii-3b. [sptrembl;acc:o75609] Ranked 207.646 212.891 1.02526
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Squared 19317.7 21958.6 1.13671
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Rooted 62.5668 65.4521 1.04612
1207 fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Measured 5946.33 6459.79 1.08635
homeobox protein dlx-2. [swissprot;acc:q07687] Squared 19317.7 21958.6 1.13671
p10-binding protein. [refseq;acc:nm_024491] Rooted 60.7029 63.5018 1.04611
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643] Ranked 207.644 212.888 1.02525
1208 homeobox protein dlx-5. [swissprot;acc:p56178] Squared 19317.7 21958.6 1.13671
meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Measured 5913.73 6423.98 1.08628
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Rooted 64.7526 67.7372 1.04609
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Ranked 224.878 219.342 1.02524
1209 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] Measured 5420.87 5887.53 1.08609
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Squared 19317.7 21958.6 1.13671
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Rooted 61.3914 64.2183 1.04605

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/