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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 1892 in total

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

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\hline
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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
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
Squared\vspace{3pt}}\\\cline{3-3}
&&\parbox{\wcC}{\vspace{3pt}\noindent
Rooted\vspace{3pt}}\\\hline
\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
activin receptor type i precursor (ec 2.7.1.37) (actr-i) (serine/threonine-protein kinase receptor r1) (skr1) (activin receptor-like kinase 2) (alk-2) (tgf-b superfamily receptor type i) (tsr-i). [source:swissprot;acc:q04771]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3050\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\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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adaptor protein with pleckstrin homology and src homology 2 domains. [source:refseq;acc:nm\_020979]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2870\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
aldehyde dehydrogenase 7 (ec 1.2.1.5). [source:swissprot;acc:p43353]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3222\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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aldehyde dehydrogenase 8 (ec 1.2.1.5). [source:swissprot;acc:p48448]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2992\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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\multirow{4}{*}{\parbox{\wcA}{\vspace{3pt}\noindent
aldehyde oxidase (ec 1.2.3.1). [source:swissprot;acc:q06278]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2960\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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&&\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
alpha crystallin a chain. [source:swissprot;acc:p02489]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2875\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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alpha crystallin b chain (alpha(b)-crystallin) (rosenthal fiber component). [source:swissprot;acc:p02511]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3082\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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alveolar soft part sarcoma chromosome region, candidate 1; aspl protein; renal cell carcinoma gene on chromosome 17; renal cell carcinoma, papillary, 17 gene; aspscr1/tfe3 fusion gene, included. [source:refseq;acc:nm\_024083]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2829\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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Ranked\vspace{3pt}}\\\cline{3-3}
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&&\parbox{\wcC}{\vspace{3pt}\noindent
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amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm\_006380]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
3191\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [source:swissprot;acc:o95376]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2798\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [source:swissprot;acc:p18859]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2893\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [source:swissprot;acc:o75964]\vspace{3pt}}}&\multirow{4}{*}{\parbox{\wcB}{\vspace{3pt}\noindent
2834\vspace{3pt}}}&\parbox{\wcC}{\vspace{3pt}\noindent
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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/