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 658 to 707 of 3228 in total 
Value Type: Ranked
Network Comparison Type: Divided
Interaction Map: High confidence
Filtered: 1

\def\wcA{0.16666666666667\textwidth}
\def\wcB{0.16666666666667\textwidth}
\def\wcC{0.16666666666667\textwidth}
\def\wcD{0.16666666666667\textwidth}
\def\wcE{0.16666666666667\textwidth}
\begin{longtable}{|c|c|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
red\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
green\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
network\_comparison\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
658\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm\_032468]\vspace{3pt}}&\multirow{12}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
229.072\vspace{3pt}}}&\multirow{12}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
216.576\vspace{3pt}}}&\multirow{12}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.0577\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
659\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
660\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
actin binding lim protein 2. [source:refseq;acc:nm\_032432]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
661\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm\_014571]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
662\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
synapsin ii. [source:swissprot;acc:q92777]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
663\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial ribosome recycling factor. [source:refseq;acc:nm\_138777]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
664\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [source:swissprot;acc:p50542]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
665\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [source:refseq;acc:nm\_012259]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
666\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [source:swissprot;acc:q14469]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
667\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [source:swissprot;acc:q13011]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
668\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [source:refseq;acc:nm\_002313]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
669\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
synapsin i (brain protein 4.1). [source:swissprot;acc:p17600]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
670\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
autoantigen ngp-1. [source:swissprot;acc:q13823]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
250.302\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
236.817\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05694\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
671\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleotide-binding protein 1 (nbp 1). [source:swissprot;acc:p53384]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
210.739\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
199.398\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05688\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
672\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
673\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
226.497\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
214.355\vspace{3pt}}}&\multirow{3}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05664\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
674\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm\_152794]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
675\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
single-minded homolog 1. [source:swissprot;acc:p81133]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
676\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [source:swissprot;acc:p52433]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
232.469\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
245.613\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05654\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
677\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
228.944\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
216.745\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05628\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
678\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sorting nexin 5. [source:swissprot;acc:q9y5x3]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
208.482\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
220.175\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05609\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
679\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]\vspace{3pt}}&\multirow{9}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
132.413\vspace{3pt}}}&\multirow{9}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
125.389\vspace{3pt}}}&\multirow{9}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05602\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
680\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
681\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
682\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
683\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
684\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
685\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
686\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
687\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm\_016246]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
688\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [source:swissprot;acc:o15514]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
237.554\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
250.823\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05586\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
689\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
135.379\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
128.225\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05579\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
690\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
220.593\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
208.987\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05553\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
691\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm\_005872]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
217.602\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
206.195\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05532\vspace{3pt}}}\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
692\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm\_001253]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
693\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [source:swissprot;acc:p51513]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
222.554\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
234.847\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05524\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
694\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [source:swissprot;acc:q07864]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
241.907\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
229.35\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05475\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
695\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [source:refseq;acc:nm\_139126]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
226.135\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
214.405\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05471\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
696\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
sr rich protein. [source:refseq;acc:nm\_032870]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
225.293\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
213.64\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05455\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
697\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ferritin heavy chain (ferritin h subunit). [source:swissprot;acc:p02794]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
220.444\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
209.113\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
1.05419\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
698\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [source:refseq;acc:nm\_177478]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
220.437\vspace{3pt}}&\multirow{10}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
209.118\vspace{3pt}}}&\multirow{10}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
1.05413\vspace{3pt}}}\\\cline{1-3}
\parbox{\wcA}{\vspace{3pt}\noindent
699\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cellular repressor of e1a-stimulated genes 2. [source:refseq;acc:nm\_153836]\vspace{3pt}}&\multirow{9}{*}{\parbox{\wcC}{\vspace{3pt}\noindent
220.438\vspace{3pt}}}&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
700\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [source:sptrembl;acc:q9byw6]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
701\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [source:swissprot;acc:o14490]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
702\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:o43865]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
703\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
limkain b1. [source:refseq;acc:nm\_019081]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
704\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [source:swissprot;acc:q96hn2]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
705\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
cellular repressor of e1a-stimulated genes. [source:refseq;acc:nm\_003851]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
706\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [source:swissprot;acc:o95886]\vspace{3pt}}&&&\\\cline{1-2}
\parbox{\wcA}{\vspace{3pt}\noindent
707\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [source:swissprot;acc:p01042]\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/