Visitors   Views   Downloads
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

A peer-reviewed article of this Preprint also exists.

View peer-reviewed version

Supplemental Information

The hESC putative interactomes

The hESC EC+TF putative interactomes A) ALL and B) C+S (C: common part; S: specific part). (Cytoscape file)

DOI: 10.7287/peerj.preprints.415v2/supp-1

List of mRNAs forming hESC and hESC-derived transcriptomes

Each mRNA is identified by the EntrezGene ID, the Official Gene Symbol and the full gene name. 'Transcriptome' column: transcriptome(s) or sub-transcriptome containing the mRNAs (hESC: human embryonic stem cells; Endo: endothelial cell; F: fibroblast; Mix: mixture of hESC-derived cells). Colour code (see Legend sheet) indicates different transcriptome and sub-transcriptomes. GO term column: GO terms found during the GO extraction (CA: cell adhesion; CC: cell cycle; CCo: cell communication; CS: cytoskeleton organisation; J: cell junction; EC: extracellular part; HS: heparan sulfate binding proteins; TF: transcription factor related part). (Excel file)

DOI: 10.7287/peerj.preprints.415v2/supp-2

General network parameters

ALL R is the randomised network from the ALL interactome while C+S R is the randomised network from the C+S interactome (C: common part; S: specific part; R: random). Power law of the degree distribution: <!--[if !msEquation]--> <!--[endif]--> with R2, the polynomial regression coefficient (degree 2).

DOI: 10.7287/peerj.preprints.415v2/supp-3

GO/KEGG analyses

GO Biological Processes term and KEGG pathway enrichments analysis of A) EC+TF interactomes, B) full lists of candidates and C-I) sub-sets of candidates (EC: extracellular part; TF: transcription factor related part).

DOI: 10.7287/peerj.preprints.415v2/supp-4

The complete list of candidates

Each protein is identified by its corresponding EntrezGene ID, gene acronym and full gene name. 'Transcriptome' column: transcriptome(s) or sub-transcriptome containing the corresponding mRNA (Endo: endothelial cell; F: fibroblast; Mix: mixture of hESC-derived cells). A colour code is applied to aid recognition of each transcriptome and sub-transcriptome (see the Legend sheet). GO term column: GO terms found during the GO term analysis (CA: cell adhesion; CC: cell cycle; CCo: cell communication; CS: cytoskeleton; J: cell junction; EC: extracellular part; HS: heparan sulfate binding proteins; TF: transcription factor related part). "Hubs" column: indicates the number of edges associated with each hub protein. 'S/C' and 'EC/TF' columns: indicates if a protein is in the specific/common interface or extracellular/transcription factor interface respectively. A) the longest ALL_EC+TF list of candidates, B) the random list, C) the ALL_EC list, D) the C+S_EC+TF list and E) the shortest C+S_EC list of candidate proteins, in which C = common part and S = specific part. (Excel file)

DOI: 10.7287/peerj.preprints.415v2/supp-5

Additional Information

Competing Interests

We declare no competing interests.

Author Contributions

Virginie Mournetas conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Quentin M. Nunes conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Patricia A. Murray conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Christopher M. Sanderson conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

David G. Fernig conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Funding

This work was partly funded by North West Cancer Research and BBSRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies