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Transkingdom network reveals bacterial players associated with cervical cancer gene expression program

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Transkingdom network reveals bacterial players associated with cervical cancer gene expression program https://t.co/DkJBpsgTMu
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Transkingdom network reveals bacterial players associated with cervical cancer gene expression program https://t.co/kz0VLKqZll
32 days ago
Transkingdom network reveals bacterial players associated with cervical cancer gene expression program https://t.co/OzLunxPVEq
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Supplemental Information

Shannon Alpha Diversity for different tissues

DOI: 10.7287/peerj.preprints.26957v1/supp-1

Abundances of Lactobacillus and L. crispatus in cervical cancer , HPV negative cervix and healthy vaginal microbiome

Abundances of Lactobacillus (A) and L. crispatus (B) in cervical cancer (CC) (our data), HPV negative cervix (HPV- cervix) and healthy vaginal microbiome (Healthy vagina). Abundances are represented by mean frequencies (%) data reported by published articles (PMID numbers of the source article specified for each column).

DOI: 10.7287/peerj.preprints.26957v1/supp-2

RT-qPCR for cervical cancer top BiBC genes

HeLa cells were co-cultured with either P. bivia or L. crispatus and gene expression was compared to negative treatment (PBS) of Hela cells. mRNA levels were normalized to 18S rRNA gene expression. (*p-value < 0.05, one-tailed Wilcoxon matched-pairs signed rank test).

DOI: 10.7287/peerj.preprints.26957v1/supp-3

map. biom summary. rarified table. cc otu table; cervical cancer relativized OTU table

DOI: 10.7287/peerj.preprints.26957v1/supp-5

Bipartite betweenness centrality results

DOI: 10.7287/peerj.preprints.26957v1/supp-6

Search for abundances top 5 OTU and Lactobacillus

DOI: 10.7287/peerj.preprints.26957v1/supp-7

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Khiem Chi Lam conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Dariia Vyshenska conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Jialu Hu analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Richard Rosario Rodrigues analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Anja Nilsen analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Ryszard A. Zielke contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Nicholas Samuel Brown performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Eva-Katrine Aarnes performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Aleksandra E. Sikora contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Natalia Shulzhenko conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Heidi Lyng conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Andrey Morgun conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The clinical protocol was approved by the Regional Committee for Medical Research Ethics in southern Norway (REC no. S-01129). Written informed consent was obtained from all patients.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The dataset generated and analyzed during the current study is available in Sequence Read Archive under accession no. SRP131188 (https://www.ncbi.nlm.nih.gov/sra/SRP131188)

Data Deposition

The following information was supplied regarding data availability:

The OTU tables are provided as a part of the supplementary material (see Table S2). The type of the software and the parameters that were used to generate this data are described in Materials & Methods section.

Funding

This research was supported by startup funds for AM and NS from Oregon State University (OSU), United States; The Norwegian Cancer Society grant nr 107438 - PR-2007-0179 (HL), seed grant from College of Pharmacy OSU (AM), DK103761 (NS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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