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 980 to 1029 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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\hline
\parbox{\wcA}{\vspace{3pt}\noindent
Rank\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
description\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Value Type\vspace{3pt}}\\
\hline
\hline
\parbox{\wcA}{\vspace{3pt}\noindent
3000\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
myeloblast kiaa0230 (fragment). [source:sptrembl;acc:q92626]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3001\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
ubiquitin-like protein nedd8. [source:swissprot;acc:q15843]\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
3002\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
cyclin t1 (cyclin t) (cyct1). [source:swissprot;acc:o60563]\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
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&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
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3003\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
testis specific leucine rich repeat protein. [source:refseq;acc:nm\_012472]\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
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&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3004\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [source:swissprot;acc:p14648]\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
3005\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [source:swissprot;acc:q16718]\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
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&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
3006\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
dgcr8 protein (digeorge syndrome critical region 8). [source:swissprot;acc:q8wyq5]\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
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3007\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
glioma-amplified sequence-41; numa binding protein 1. [source:refseq;acc:nm\_006530]\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
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3008\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [source:swissprot;acc:p35658]\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
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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3009\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [source:swissprot;acc:p14854]\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
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3010\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [source:swissprot;acc:p06132]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
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Ranked\vspace{3pt}}\\\cline{3-3}
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3011\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
dna replication licensing factor mcm8 (minichromosome maintenance 8). [source:swissprot;acc:q9uja3]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Ranked\vspace{3pt}}\\\cline{3-3}
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3012\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [source:swissprot;acc:p14678]\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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Ranked\vspace{3pt}}\\\cline{3-3}
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\parbox{\wcA}{\vspace{3pt}\noindent
3013\vspace{3pt}}&\parbox{\wcB}{\vspace{3pt}\noindent
major centromere autoantigen b (centromere protein b) (cenp-b). [source:swissprot;acc:p07199]\vspace{3pt}}&\parbox{\wcC}{\vspace{3pt}\noindent
Measured\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/