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 6008 to 6057 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1502 wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Rooted 64.181 66.575 1.0373
1503 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Squared 18555.4 20672 1.11407
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Measured 10075.5 9377.75 1.0744
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Ranked 242.181 237.834 1.01828
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Rooted 64.181 66.575 1.0373
1504 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Ranked 259.439 254.797 1.01822
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Measured 10075.5 9377.75 1.0744
sorting nexin 17. [swissprot;acc:q15036] Squared 18555.4 20672 1.11407
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Rooted 64.181 66.575 1.0373
1505 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Measured 10075.5 9377.75 1.0744
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Squared 20660.9 23016.9 1.11403
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Ranked 216.158 212.316 1.0181
rest corepressor. [refseq;acc:nm_015156] Rooted 64.181 66.575 1.0373
1506 60s ribosomal protein l28. [swissprot;acc:p46779] 63.0816 65.4287 1.03721
bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] Squared 20660.9 23016.9 1.11403
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Ranked 212.103 208.339 1.01807
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Measured 6152.78 6610.46 1.07439
1507 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Squared 20660.9 23016.9 1.11403
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Rooted 64.4036 66.795 1.03713
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Ranked 213.274 209.5 1.01801
1508 gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Rooted 64.4036 66.795 1.03713
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Measured 6152.78 6610.46 1.07439
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Squared 22766.5 25361.9 1.114
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Ranked 213.274 209.5 1.01801
1509 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] Measured 7237.39 7775.21 1.07431
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Squared 33294.4 37086.4 1.11389
alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] Ranked 225.148 221.177 1.01795
p47 protein isoform a. [refseq;acc:nm_016143] Rooted 64.8735 67.282 1.03713
1510 60s ribosomal protein l21. [swissprot;acc:p46778] Measured 5546.11 5957.99 1.07426
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Ranked 225.148 221.177 1.01795
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Squared 14522.9 16175.3 1.11378
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Rooted 64.4036 66.795 1.03713
1511 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Ranked 213.268 209.509 1.01794
nucleoporin like 1. [refseq;acc:nm_014089] Rooted 63.302 65.6446 1.03701
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Squared 14522.9 16175.3 1.11378
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Measured 7234.61 7771.58 1.07422
1512 rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Rooted 63.302 65.6446 1.03701
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Squared 14522.9 16175.3 1.11378
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Measured 7234.61 7771.58 1.07422
surfeit locus protein 1. [swissprot;acc:q15526] Ranked 213.268 209.509 1.01794
1513 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Rooted 63.302 65.6446 1.03701
cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Ranked 213.268 209.509 1.01794
oligophrenin 1. [swissprot;acc:o60890] Squared 14522.9 16175.3 1.11378
proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Measured 6079.65 6530.82 1.07421
1514 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] Rooted 63.609 65.9615 1.03698
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] Measured 7232.14 7768.35 1.07414
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Squared 2547.12 2286.96 1.11376
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Ranked 213.268 209.509 1.01794
1515 af-6 protein. [swissprot;acc:p55196] Rooted 61.7453 64.0287 1.03698

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/