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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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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1777 to 1826 of 1892 in total

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

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Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Value Type\vspace{3pt}}\\
\hline
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\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3200\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
endosome-associated fyve-domain protein. [source:refseq;acc:nm\_014733]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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3201\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
recessive polycystic kidney disease protein tg737 homolog. [source:swissprot;acc:q13099]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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3202\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [source:refseq;acc:nm\_007322]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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3203\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [source:swissprot;acc:o15347]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
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3204\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
vaccinia related kinase 2; vaccinia-related kinase-2. [source:refseq;acc:nm\_006296]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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3205\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
rb1-inducible coiled coil protein 1. [source:refseq;acc:nm\_014781]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
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3206\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [source:swissprot;acc:q9by42]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
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3207\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
complement component c8 beta chain precursor. [source:swissprot;acc:p07358]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
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\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3208\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [source:swissprot;acc:q13761]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
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3209\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [source:swissprot;acc:p51948]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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3210\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
trabid protein. [source:swissprot;acc:q9ugi0]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
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3211\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [source:swissprot;acc:q07973]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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3212\vspace{3pt}}}&\multirow{2}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
rala binding protein 1; rala-binding protein. [source:refseq;acc:nm\_006788]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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Ranked\vspace{3pt}}\\\hline
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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/