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 825 to 874 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
413 dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Divided 240.913 261.45 1.08525
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Subtracted 223.202 205.9 17.302
414 katanin p60 subunit a 1. [refseq;acc:nm_007044] Divided 232.431 252.238 1.08522
max protein. [swissprot;acc:p25912] Subtracted 227.828 210.561 17.267
415 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Divided 232.382 252.166 1.08514
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Subtracted 200.586 183.423 17.163
416 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Divided 240.6 261.041 1.08496
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] Subtracted 200.791 183.66 17.131
417 set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Divided 233.539 253.197 1.08417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 235.94 218.837 17.103
418 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Divided 233.539 253.197 1.08417
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Subtracted 233.723 216.674 17.049
419 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Divided 233.539 253.197 1.08417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Subtracted 235.922 218.925 16.997
420 cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Divided 233.539 253.197 1.08417
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Subtracted 238.704 255.68 16.976
421 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Divided 223.202 205.9 1.08403
422 ras-related protein rab-37. [swissprot;acc:q96ax2] 240.287 260.193 1.08284
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Subtracted 238.704 255.68 16.976
423 oligophrenin 1. [swissprot;acc:o60890]
ras-related protein rab-26. [swissprot;acc:q9ulw5] Divided 240.287 260.193 1.08284
424 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Subtracted 251.83 234.951 16.879
425 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 16.864
max protein. [swissprot;acc:p25912] Divided 227.828 210.561 1.082
426 dynactin 4. [refseq;acc:nm_032486] 233.142 252.253 1.08197
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Subtracted 212.547 229.411 16.864
427 dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Divided 239.977 259.525 1.08146
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Subtracted 212.547 229.411 16.864
428 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Divided 253.852 234.808 1.0811
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Subtracted 227.748 210.888 16.86
429 polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Divided 239.709 259.038 1.08064
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Subtracted 251.344 234.514 16.83
430 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 250.938 234.134 16.804
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Divided 227.748 210.888 1.07995
431 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Subtracted 233.529 216.737 16.792
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Divided 236.245 255.113 1.07987
432 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 1.07934
mct-1 protein. [refseq;acc:nm_014060] Subtracted 226.313 243.03 16.717
433 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Divided 212.547 229.411 1.07934
434 ad24 protein. [refseq;acc:nm_022451] Subtracted 251.334 234.672 16.662
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Divided 212.547 229.411 1.07934
435 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 221.522 205.286 1.07909
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Subtracted 251.299 234.729 16.57
436 paxillin. [swissprot;acc:p49023] Divided 221.522 205.286 1.07909
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Subtracted 231.496 248.048 16.552
437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Divided 209.921 226.459 1.07878
Subtracted 16.538

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/