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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Interaction Map Value Type Gene Filtered Rank description green Network Comparison Type red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 29840 in total
Interaction Map  : High confidence
Value Type  : Measured
Filtered  : 0
Rank
description
green
Network Comparison Type
red
network_comparison
226 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 758.411 Divided 658.544 1.15165
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 1079.37 Subtracted 1225.09 145.72
227 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 1225.08 145.71
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 369.011 Divided 424.258 1.14972
228 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 1079.37 Subtracted 1225.08 145.71
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 4696.36 Divided 4089.65 1.14835
229 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 368.317 320.752 1.14829
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 1079.38 Subtracted 1225.08 145.7
230 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 1718.6 Divided 1498.17 1.14713
231 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 1759.22 2017.91 1.14705
espin. [refseq;acc:nm_031475] 1079.38 Subtracted 1225.07 145.69
232 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 1906.28 Divided 1663.73 1.14579
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 2220.68 Subtracted 2075.64 145.04
233 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 6303 6158 145
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 399.534 Divided 348.823 1.14538
234 keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 1079.77 Subtracted 1224.65 144.88
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 4550.64 Divided 5202.89 1.14333
235 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 2255.28 Subtracted 2113.27 142.01
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 1843.92 Divided 1612.86 1.14326
236 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 1908.13 Subtracted 1766.66 141.47
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 3103.01 Divided 2715.75 1.1426
237 germ cell-less. [refseq;acc:nm_022471] 1694.05 Subtracted 1829.81 135.76
p28 ing5. [refseq;acc:nm_032329] 2243.69 Divided 2551.23 1.13707
238 casein kinase i alpha s-like. [refseq;acc:nm_145203] 1933.94 2198.47 1.13678
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 359.631 Subtracted 494.417 134.786
239 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 434.366 Divided 382.142 1.13666
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] 11305 Subtracted 11170.7 134.3
240 putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 1676.18 Divided 1475.83 1.13575
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 771.309 Subtracted 903.967 132.658
241 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 3481.87 3614.24 132.37
keratin associated protein 9.2. [refseq;acc:nm_031961] 1079.01 Divided 1225.47 1.13574
242 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 1161.64 Subtracted 1293.73 132.09
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 642.343 Divided 729.216 1.13524
243 dead-box protein. [refseq;acc:nm_018665] 183 Subtracted 313.667 130.667
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 1079.36 Divided 1225.09 1.13502
244 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 1205.1 Subtracted 1334.19 129.09
245 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 421 292 129
keratin associated protein 1.5. [refseq;acc:nm_031957] 1079.36 Divided 1225.09 1.13502
246 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 279.24 Subtracted 150.673 128.567
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 1079.36 Divided 1225.09 1.13502
247 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 142.981 Subtracted 271.484 128.503
248 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 2452.23 2323.8 128.43
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 1079.37 Divided 1225.09 1.135
249 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] 2452.23 Subtracted 2323.8 128.43
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 1079.37 Divided 1225.08 1.135
250 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]
ptd016 protein. [refseq;acc:nm_016125] 158 Subtracted 30 128

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/