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 2377 to 2426 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1189 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] High confidence 209.649 204.406 1.02565
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Low confidence 195.344 190.932 1.02311
1190 bleomycin hydrolase (ec 3.4.22.40) (blm hydrolase) (bmh) (bh). [swissprot;acc:q13867] 202.963 198.378
ubiquitin. [swissprot;acc:p02248] High confidence 209.6 204.372 1.02558
1191 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 220.742 215.237
zinc finger protein gli3. [swissprot;acc:p10071] Low confidence 203.052 198.466 1.02311
1192 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 199.02 194.529 1.02309
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] High confidence 220.742 215.237 1.02558
1193 lbp-9. [refseq;acc:nm_014553]
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Low confidence 201.092 196.553 1.02309
1194 dna replication licensing factor mcm2 (nuclear protein bm28). [swissprot;acc:p49736] 202.182 197.621 1.02308
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] High confidence 220.742 215.237 1.02558
1195 85 kda calcium-independent phospholipase a2 (ec 3.1.1.4) (ipla2) (cai- pla2) (group vi phospholipase a2) (gvi pla2). [swissprot;acc:o60733] Low confidence 202.297 197.738 1.02306
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] High confidence 269.608 276.493 1.02554
1196 kinesin protein. [refseq;acc:nm_032559] 224.858 219.264 1.02551
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Low confidence 202.297 197.738 1.02306
1197 mstp028 protein. [refseq;acc:nm_031954] High confidence 219.042 213.6 1.02548
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, delta isoform (pp2a, b subunit, b' delta isoform) (pp2a, b subunit, b56 delta isoform) (pp2a, b subunit, pr61 delta isoform) (pp2a, b subunit, r5 delta isoform). [swissprot;acc:q14738] Low confidence 202.297 197.738 1.02306
1198 serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, gamma isoform (pp2a, b subunit, b' gamma isoform) (pp2a, b subunit, b56 gamma isoform) (pp2a, b subunit, pr61 gamma isoform) (pp2a, b subunit, r5 gamma isoform). [swissprot;acc:q13362]
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] High confidence 269.59 276.454 1.02546
1199 u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] 241.496 235.508 1.02543
wd-repeat protein 4. [swissprot;acc:p57081] Low confidence 204.517 199.909 1.02305
1200 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 198.973 194.493 1.02303
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] High confidence 219.03 213.604 1.0254
1201 dna repair protein rad52 homolog. [swissprot;acc:p43351] Low confidence 203.852 199.266 1.02301
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] High confidence 210.986 216.344 1.0254
1202 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 227.274 233.041 1.02537
phosphatidylinositol glycan class t precursor. [refseq;acc:nm_015937] Low confidence 204.636 200.036 1.023
1203 protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [refseq;acc:nm_015886] 203.323 198.756 1.02298
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] High confidence 219.023 213.606 1.02536
1204 polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863] 219.022 213.607 1.02535
r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491] Low confidence 203.323 198.756 1.02298
1205 nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] 197.84 193.402 1.02295
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] High confidence 224.805 219.251 1.02533
1206 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Low confidence 203.629 208.303 1.02295
integral membrane protein cii-3b. [sptrembl;acc:o75609] High confidence 207.646 212.891 1.02526
1207 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Low confidence 197.868 193.428 1.02295
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] High confidence 207.644 212.888 1.02525
1208 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Low confidence 197.863 193.425 1.02294
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] High confidence 224.878 219.342 1.02524
1209 guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Low confidence 202.873 198.325 1.02293
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912] High confidence 207.931 213.175 1.02522
1210 kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] 224.764 219.241 1.02519
snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966] Low confidence 202.718 198.176 1.02292
1211 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] 201.559 197.042
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] High confidence 214.364 219.759 1.02517
1212 kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]
microfibrillar-associated protein 1. [swissprot;acc:p55081] Low confidence 202.718 198.176 1.02292
1213 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] High confidence 214.364 219.759 1.02517
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Low confidence 198.145 193.707 1.02291

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/