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 3068 to 3117 of 3228 in total
Value Type: Measured
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1
red: 0.00001
green: 0.00001
network\_comparison: 1
\def\wcA{0.33333333333333\textwidth} \def\wcB{0.33333333333333\textwidth} \begin{longtable}{|c|c|} \hline \parbox{\wcA}{\vspace{3pt}\noindent Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent description\vspace{3pt}}\\ \hline \hline \parbox{\wcA}{\vspace{3pt}\noindent 3068\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent headcase homolog; hhdc for homolog of drosophila headcase. [source:refseq;acc:nm\_016217]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3069\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent bone morphogenetic protein 5 precursor (bmp-5). [source:swissprot;acc:p22003]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3070\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent mam domain containing glycosylphosphatidylinositol anchor 1; glycosyl-phosphatidyl-inositol-mam. [source:refseq;acc:nm\_153487]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3071\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent serine/threonine kinase 38; serine threonine protein kinase. [source:refseq;acc:nm\_007271]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3072\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [source:refseq;acc:nm\_017906]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3073\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm\_015952]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3074\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent tu12b1-ty protein. [source:refseq;acc:nm\_016575]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3075\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [source:swissprot;acc:p45974]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3076\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent placental protein 11 precursor (ec 3.4.21.-) (pp11). [source:swissprot;acc:p21128]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3077\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent h2a histone family, member j isoform 1. [source:refseq;acc:nm\_018267]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3078\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent camp responsive element binding protein-like 2. [source:refseq;acc:nm\_001310]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3079\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3080\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [source:swissprot;acc:q99733]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3081\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [source:swissprot;acc:o75489]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3082\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3083\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent glycine receptor beta chain precursor (glycine receptor 58 kda subunit). [source:swissprot;acc:p48167]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3084\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [source:swissprot;acc:q9uha4]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3085\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [source:swissprot;acc:p36537]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3086\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [source:swissprot;acc:p54855]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3087\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [source:swissprot;acc:p09972]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3088\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent 14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [source:swissprot;acc:p42655]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3089\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [source:swissprot;acc:p10644]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3090\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent enhancer of zeste homolog 1 (enx-2). [source:swissprot;acc:q92800]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3091\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transcription factor-like protein 4 (max-like bhlhzip protein) (bigmax protein) (mlx). [source:swissprot;acc:q9uh92]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3092\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent developmentally regulated gtp-binding protein 2 (drg 2). [source:swissprot;acc:p55039]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3093\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ptd016 protein. [source:refseq;acc:nm\_016125]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3094\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [source:swissprot;acc:q16763]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3095\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent erythroid differentiation-related factor 1. [source:refseq;acc:nm\_015608]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3096\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nucleoplasmin 3. [source:swissprot;acc:o75607]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3097\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent sec23-interacting protein p125; phospholipase. [source:refseq;acc:nm\_007190]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3098\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent enhancer of zeste homolog 2 (enx-1). [source:swissprot;acc:q15910]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3099\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent caveolin-1. [source:swissprot;acc:q03135]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3100\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [source:refseq;acc:nm\_172341]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3101\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent gamma-interferon inducible lysosomal thiol reductase precursor (gamma-interferon-inducible protein ip-30). [source:swissprot;acc:p13284]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3102\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent protein cgi-140 (protein ptd008) (my006 protein). [source:swissprot;acc:q9y284]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3103\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [source:swissprot;acc:p18858]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3104\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent glioma tumor suppressor candidate region gene 2 protein (p60). [source:swissprot;acc:q9nzm5]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3105\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent transforming growth factor beta 1 precursor (tgf-beta 1). [source:swissprot;acc:p01137]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3106\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [source:refseq;acc:nm\_017432]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3107\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent lyl-1 protein (lymphoblastic leukemia derived sequence 1). [source:swissprot;acc:p12980]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3108\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent sorting nexin 16. [source:swissprot;acc:p57768]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3109\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [source:refseq;acc:nm\_003882]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3110\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ras-related protein rab-2a. [source:swissprot;acc:p08886]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3111\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent serine/threonine protein kinase 3 (ec 2.7.1.37) (ste20-like kinase mst2) (mst-2) (mammalian ste20-like protein kinase 2) (serine/threonine protein kinase krs-1). [source:swissprot;acc:q13188]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3112\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ras-related protein rab-11a (rab-11) (24kg) (yl8). [source:swissprot;acc:p24410]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3113\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [source:swissprot;acc:p13662]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3114\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent regulatory protein tsc-22 (tgfb stimulated clone 22 homolog). [source:swissprot;acc:q15714]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3115\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent serine/threonine protein kinase 24 (ec 2.7.1.37) (ste20-like kinase mst3) (mst-3) (mammalian ste20-like protein kinase 3). [source:swissprot;acc:q9y6e0]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3116\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent mo25-like protein. [source:swissprot;acc:q9h9s4]\vspace{3pt}}\\\hline \parbox{\wcA}{\vspace{3pt}\noindent 3117\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent ba203i16.1 (hypothetical protein kiaa0970). [source:sptrembl;acc:q9h1w1]\vspace{3pt}}\\\hline nd{longtable}
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/