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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Gene description Rank Value Type Network Comparison Type red Filtered Interaction Map green network_comparison

Results: HTML CSV LaTeX

Showing element 1 to 50 of 1892 in total

Network Comparison Type: Subtracted
red: 0
Filtered: 1
Interaction Map: High confidence
green: 0
network\_comparison: 0

\def\wcA{0.25\textwidth}
\def\wcB{0.25\textwidth}
\def\wcC{0.25\textwidth}
\begin{longtable}{|c|c|c|}
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Value Type\vspace{3pt}}\\
\hline
\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [source:swissprot;acc:q15147]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3126\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [source:swissprot;acc:o75891]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2922\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\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}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3088\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [source:swissprot;acc:p15428]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2855\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\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}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3079\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [source:refseq;acc:nm\_025193]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3147\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3 beta-hydroxysteroid dehydrogenase (fragments). [source:sptrembl;acc:q9udk8]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2756\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [source:swissprot;acc:p14060]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2802\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [source:swissprot;acc:q99714]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3180\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [source:swissprot;acc:q03393]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2904\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
60s ribosomal protein l37a. [source:swissprot;acc:p12751]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2959\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [source:swissprot;acc:q05084]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3227\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{2}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [source:swissprot;acc:p24588]\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2788\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\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/