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Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

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RT @outinsight: My first preprint
My first preprint
35 days ago
Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining https://t.co/eyHoVj7uo9
Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining https://t.co/adNo9Xi7Wt
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Supplemental Information

Individual and merged networks

Cytoscape file containing independent and merged networks. Opens with Cytoscape 3.1

DOI: 10.7287/peerj.preprints.3472v1/supp-1

Annotations

Text-file describing the annotations in the Cytoscape files

DOI: 10.7287/peerj.preprints.3472v1/supp-2

Script for identifying candidate genes

Python file containing candidate gene script

DOI: 10.7287/peerj.preprints.3472v1/supp-3

Script for identifying hypothetical genes

Python file containing hypothetical gene script

DOI: 10.7287/peerj.preprints.3472v1/supp-4

Annotations from EVEX

Text-file containing annotations from EVEX/Cyanobase

DOI: 10.7287/peerj.preprints.3472v1/supp-5

First neighbor GBA and script-based clusters

Cytoscape file containing the first neighbour GBA and script-based clusters used in the case studies. Opens with Cytoscape 3.1

DOI: 10.7287/peerj.preprints.3472v1/supp-6

Cytoscape file with identified motifs

Cytoscape file containing all genes in the genome of Synechocystis 6803 without an annotation that forms a motif with at least two other nodes via at least two different data-types (i.e. edges), of which one is direct and the second is indirect, and at least one of the members of the motif has an existing annotation. Opens with Cytoscape 3.1

DOI: 10.7287/peerj.preprints.3472v1/supp-7

List of candidate genes

Text-file containing list of possible candidates of hypotheticals

DOI: 10.7287/peerj.preprints.3472v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Sanna M Kreula conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Suwisa Kaewphan conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Filip Ginter conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Patrik R Jones conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Funding

This work was supported by Emil Aaltosen säätiö (Kreula, S.), Academy of Finland projects no. 253269 (Jones, P.R., Kreula, S) and no. 138796 (Ginter, F.), ATT Tieto kayttöön grant (Kaewphan, S.), and the Finnish Cultural Foundation, Satakunta Regional fund (Kreula, S.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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