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 3158 to 3207 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
790 melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194] Squared 27407.7 31927.7 1.16492
parafibromin. [refseq;acc:nm_024529] Rooted 53.2852 56.7723 1.06544
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Measured 5890.88 6548.28 1.1116
791 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Squared 27407.7 31927.7 1.16492
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Rooted 62.5007 58.6648 1.06539
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Ranked 224.244 234.511 1.04578
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Measured 4025.3 4474.3 1.11154
792 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 6772.75 7526.2 1.11125
calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] Squared 27407.7 31927.7 1.16492
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] Ranked 224.244 234.511 1.04578
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Rooted 63.8039 67.9633 1.06519
793 acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] Squared 27407.7 31927.7 1.16492
beta-catenin (pro2286). [swissprot;acc:p35222] Rooted 60.2378 64.1631 1.06516
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Ranked 224.244 234.511 1.04578
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Measured 5036.92 5596.36 1.11107
794 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Rooted 57.9449 61.719 1.06513
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Squared 29554.6 34419.4 1.1646
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Measured 6441.17 7154.55 1.11075
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Ranked 224.244 234.511 1.04578
795 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Measured 6441.14 7154.13 1.11069
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Rooted 52.1577 48.9787 1.06491
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Squared 29554.6 34419.4 1.1646
serpin b11. [swissprot;acc:q96p15] Ranked 224.244 234.511 1.04578
796 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Measured 6834.54 7590.49 1.11061
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Ranked 224.244 234.511 1.04578
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Rooted 54.765 51.4319 1.06481
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Squared 25842.1 30093.4 1.16451
797 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] Ranked 224.244 234.511 1.04578
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Measured 6834.54 7590.49 1.11061
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Squared 22535.2 26238.4 1.16433
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Rooted 54.1622 57.6725 1.06481
798 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 54.765 51.4319
leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Ranked 224.244 234.511 1.04578
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Squared 22587.2 26296.1 1.1642
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Measured 6834.54 7590.49 1.11061
799 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Rooted 54.765 51.4319 1.06481
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Squared 22623.7 26336.8 1.16412
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Ranked 221.965 212.404 1.04501
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Measured 6834.54 7590.49 1.11061
800 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Rooted 54.1622 57.6725 1.06481
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Ranked 221.965 212.404 1.04501
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Measured 6075.55 6746.92 1.1105
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Squared 22210.6 25839.9 1.1634
801 beta-catenin (pro2286). [swissprot;acc:p35222] Ranked 224.445 214.894 1.04445
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Rooted 54.765 51.4319 1.06481
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Measured 6456.35 7169.75 1.1105
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Squared 22208.7 25833.6 1.16322
802 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 20131.3 23416.5 1.16319
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Measured 6455.66 7168.82 1.11047
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 221.785 1.04425

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/