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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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 1051 to 1100 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{2}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
placenta growth factor precursor (plgf). [source:swissprot;acc:p49763]\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3036\vspace{3pt}}}&\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
placental protein 11 precursor (ec 3.4.21.-) (pp11). [source:swissprot;acc:p21128]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3076\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
platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [source:swissprot;acc:p43034]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3221\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
pogo transposable element with znf domain isoform 1. [source:refseq;acc:nm\_015100]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2932\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
polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [source:refseq;acc:nm\_024947]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2809\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
postsynaptic protein cript; hspc139 protein. [source:refseq;acc:nm\_014171]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3034\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
potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [source:refseq;acc:nm\_016121]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2975\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
prefoldin subunit 4 (protein c-1). [source:swissprot;acc:q9nqp4]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3130\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
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [source:refseq;acc:nm\_172341]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3100\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
prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [source:swissprot;acc:q9nrd5]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3143\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
programmed cell death 10; apoptosis-related protein 15. [source:refseq;acc:nm\_007217]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3052\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
prostate tumor overexpressed gene 1; prostate tumor over expressed gene 1. [source:refseq;acc:nm\_017432]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3106\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
protease inhibitor 15 preproprotein; 25 kda trypsin inhibitor. [source:refseq;acc:nm\_015886]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2966\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
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/