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 6308 to 6357 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
789 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Rooted Subtracted 58.4551 62.5601 4.105
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Squared 28579.3 32606.7 4027.4
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Measured 6167.33 6785.98 618.65
midasin (midas-containing protein). [swissprot;acc:q9nu22] Rooted Divided 54.2779 57.8311 1.06546
unr protein. [swissprot;acc:o75534] Ranked Subtracted 230.087 220.579 9.508
790 40s ribosomal protein s21. [swissprot;acc:p35265] Divided 224.244 234.511 1.04578
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Squared Subtracted 28578.7 32605.8 4027.1
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194] Divided 27407.7 31927.7 1.16492
parafibromin. [refseq;acc:nm_024529] Rooted 53.2852 56.7723 1.06544
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Subtracted 65.1512 69.252 4.1008
ran-gtp binding protein (fragment). [sptrembl;acc:o60518] Measured 6165.1 6783.01 617.91
testis-specific protein tex28. [swissprot;acc:o15482] Ranked 212.386 221.785 9.399
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 Divided 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
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Subtracted 26005.2 30020.3 4015.1
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Rooted Divided 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
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Measured Subtracted 6544.26 7159.43 615.17
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Rooted 65.0565 69.1533 4.0968
similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] Ranked 212.386 221.785 9.399
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Measured Divided 4025.3 4474.3 1.11154
792 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] Squared Subtracted 28551.5 32561.8 4010.3
a kindred of iglon. [refseq;acc:nm_173808] Ranked 212.386 221.785 9.399
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Measured Divided 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
target of myb protein 1. [swissprot;acc:o60784] Measured Subtracted 5640.79 6255.85 615.06
tubby protein homolog. [swissprot;acc:p50607] Rooted 65.0565 69.1533 4.0968
793 acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] Squared Divided 27407.7 31927.7 1.16492
ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1] Ranked Subtracted 212.386 221.785 9.399
beta-catenin (pro2286). [swissprot;acc:p35222] Rooted Divided 60.2378 64.1631 1.06516
bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Ranked 224.244 234.511 1.04578
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] Measured Subtracted 5641.11 6255.99 614.88
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Squared 23894.7 27894.5 3999.8
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Rooted 65.0565 69.1533 4.0968
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Measured Divided 5036.92 5596.36 1.11107
794 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Squared Subtracted 26705.9 30699 3993.1
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Rooted Divided 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
inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] Ranked Subtracted 212.386 221.785 9.399
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Rooted 65.0565 69.1533 4.0968
plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Ranked Divided 224.244 234.511 1.04578
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Measured Subtracted 5641.12 6255.99 614.87
795 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Squared 23958.6 27945.1 3986.5
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Measured Divided 6441.14 7154.13 1.11069
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897] Ranked Subtracted 212.386 221.785 9.399
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Rooted Divided 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

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/