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 Hugo Value Type description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 475 to 502 of 502 in total 
Value Type: Ranked
Network Comparison Type: Divided
Filtered: 0
Interaction Map: High confidence

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\def\wcE{0.14285714285714\textwidth}
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\begin{longtable}{|c|c|c|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Hugo\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
red\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
green\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
network\_comparison\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
475\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
18667\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
18500\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00903\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
476\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
atlastin; guanylate-binding protein 3. [source:refseq;acc:nm\_015915]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
8403\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
8329\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00888\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
477\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [source:swissprot;acc:p47986]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
15920\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
15780.2\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00886\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
478\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ACAA1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [source:swissprot;acc:p09110]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
10156.4\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
10243.1\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00854\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
479\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
ALDH3B2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
15155.8\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
15031.7\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
1.00826\vspace{3pt}}}\\\cline{1-3}
\parbox{\wcA}{\vspace{3pt}\noindent
480\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
C6orf35\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
uncharacterized bone marrow protein bm033. [source:refseq;acc:nm\_018452]\vspace{3pt}}&&&\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
481\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
uridine kinase-like 1. [source:swissprot;acc:q9nwz5]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
11554.3\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
11462.4\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00802\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
482\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
kinesin-like protein kif13b (kinesin-like protein gakin). [source:swissprot;acc:q9nqt8]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
6156.33\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
6205.67\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00801\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
483\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
12223.8\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
12127.5\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00794\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
484\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SLMO2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
protein c20orf45 (cgi-107). [source:swissprot;acc:q9y3b1]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
11489.7\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
11414.3\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00661\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
485\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
pepsin a precursor (ec 3.4.23.1). [source:swissprot;acc:p00790]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
12461.5\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
12542.3\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00648\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
486\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
PRPF40B\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
huntingtin interacting protein c. [source:refseq;acc:nm\_012272]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
13372.4\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
13288.3\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00633\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
487\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
survival motor neuron protein (component of gems 1) (gemin1). [source:swissprot;acc:q16637]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
13236.8\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
13159.3\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00589\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
488\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
heat shock factor binding protein 1. [source:swissprot;acc:o75506]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
15204.2\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
15127.8\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00505\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
489\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SHCBP1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm\_024745]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
8854.04\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
8811.09\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00487\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
490\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
10388.7\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
10338.7\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00484\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
491\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
RWDD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
rwd domain containing 1; ptd013 protein; cgi-24 protein. [source:refseq;acc:nm\_015952]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
21970\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
21880\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00411\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
492\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
SMARCD1\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [source:swissprot;acc:q96gm5]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
6802.96\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
6829.74\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00394\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
493\vspace{3pt}}&\multirow{6}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [source:sptrembl;acc:q9h5b6]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
11999.1\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
12041.7\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00355\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
494\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
11985.5\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
11959.4\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00218\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
495\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [source:swissprot;acc:o00232]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
11725.2\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
11748.1\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00195\vspace{3pt}}\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
496\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
9394\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
9411.49\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
1.00186\vspace{3pt}}}\\\cline{1-1}\cline{3-5}
\parbox{\wcA}{\vspace{3pt}\noindent
497\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [source:refseq;acc:nm\_014633]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
13692.7\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
13718.2\vspace{3pt}}&\\\cline{1-1}\cline{3-6}
\parbox{\wcA}{\vspace{3pt}\noindent
498\vspace{3pt}}&&\parbox{\wcC}{\vspace{3pt}\noindent
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
10231.8\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
10248.3\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00161\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
499\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
IMPDH2\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [source:swissprot;acc:p12268]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
9080.73\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
9069.58\vspace{3pt}}&\parbox{\wcF}{\vspace{3pt}\noindent
1.00123\vspace{3pt}}\\\hline
\parbox{\wcA}{\vspace{3pt}\noindent
500\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
huntingtin interacting protein e; huntingtin interactor protein e. [source:refseq;acc:nm\_007076]\vspace{3pt}}&\parbox{\wcD}{\vspace{3pt}\noindent
394\vspace{3pt}}&\parbox{\wcE}{\vspace{3pt}\noindent
394\vspace{3pt}}&\multirow{3}{*}{\parbox{\wcF}{\vspace{3pt}\noindent
1\vspace{3pt}}}\\\cline{1-5}
\parbox{\wcA}{\vspace{3pt}\noindent
501\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
HGD\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]\vspace{3pt}}&\multirow{2}{*}{\parbox{\wcD}{\vspace{3pt}\noindent
0.00001\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcE}{\vspace{3pt}\noindent
0.00001\vspace{3pt}}}&\\\cline{1-3}
\parbox{\wcA}{\vspace{3pt}\noindent
502\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
BRAP\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
brca1 associated protein. [source:refseq;acc:nm\_006768]\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

 - Hugo is the HGNC identifier if it exists

 - 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/