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 2808 to 2857 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
351 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Measured 1 17396.9 20483.9 1.17745
352 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 30682.9 38183.6 1.24446
bet3 homolog. [swissprot;acc:o43617] Measured 17396.9 20483.9 1.17745
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 0 15.4896 14.7645 1.04911
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured 48 51 1.0625
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Rooted 1 61.3354 67.8621 1.10641
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked 242.14 265.696 1.09728
353 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Squared 71383 57399.3 1.24362
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured 0 48 51 1.0625
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
mstp028 protein. [refseq;acc:nm_031954] Rooted 64.9832 62.0398 1.04744
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 1 61.3354 67.8623 1.10641
p66 alpha. [refseq;acc:nm_017660] Measured 12839 10911.1 1.17669
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Ranked 231.73 211.252 1.09694
354 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Rooted 0 22.9129 24 1.04744
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured 48 51 1.0625
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
paraspeckle protein 1. [refseq;acc:nm_018282] 1 71360.3 57385.8 1.24352
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 234.691 257.442 1.09694
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1.17669
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 49.2848 54.5246 1.10632
355 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 0 27.6061 28.9062 1.04709
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 1 58.0752 64.23 1.10598
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 0 48 51 1.0625
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 1 15588.1 19381.8 1.24337
syntaxin 6. [swissprot;acc:o43752] Ranked 234.673 257.414 1.09691
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured 12839 10911.1 1.17669
356 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Ranked 243.24 266.796 1.09684
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Rooted 0 37.0208 38.7581 1.04693
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 48 51 1.0625
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared 1 35247.5 43820.5 1.24322
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Rooted 58.0752 64.23 1.10598
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured 11004.2 12944.2 1.1763
357 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Rooted 0 28.0711 26.8141 1.04688
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Ranked 1 243.12 266.661 1.09683
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Rooted 61.2684 67.755 1.10587
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured 5061.11 5950.22 1.17567
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 0 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 48 51 1.0625
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Squared 1 9811.86 7908.29 1.24071
358 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured 0 48 51 1.0625

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/