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 5986 to 6035 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1497 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Ranked 224.476 220.363 1.01866
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Measured 6339.08 6812.45 1.07467
fibulin-2 precursor. [swissprot;acc:p98095] Rooted 76.496 79.3591 1.03743
1498 40s ribosomal protein s13. [swissprot;acc:q02546] Measured 5414.98 5818.7 1.07456
dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] Rooted 64.2624 66.6652 1.03739
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Squared 21291.9 23721 1.11409
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Ranked 224.022 219.924 1.01863
1499 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] Rooted 64.2544 66.6549 1.03736
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Squared 21291.9 23721 1.11409
hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Measured 5798.31 6230.55 1.07455
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Ranked 224.509 220.411 1.01859
1500 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Measured 10075.5 9377.75 1.0744
cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] Ranked 213.398 209.52 1.01851
fidgetin-like 1. [refseq;acc:nm_022116] Rooted 63.2895 65.6523 1.03733
histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Squared 21291.9 23721 1.11409
1501 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 18555.4 20672 1.11407
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Measured 10075.5 9377.75 1.0744
kinesin family member c3. [refseq;acc:nm_005550] Ranked 214.727 210.838 1.01845
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Rooted 60.5617 62.8214 1.03731
1502 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Measured 10075.5 9377.75 1.0744
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Squared 18555.4 20672 1.11407
uridine kinase-like 1. [swissprot;acc:q9nwz5] Ranked 218.084 214.149 1.01838
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

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/