0000000000715559
AUTHOR
Mercedes Herrera
showing 19 related works from this author
Benchmarking plant diversity of Palaearctic grasslands and other open habitats
2021
© 2021 The Authors.
Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colorectal cancer.
2018
Exosome production from cancer-associated fibroblasts seems to be an important driver of tumor progression. We report the first in-depth biotype characterization of ncRNAs, analyzed by Next Generation Sequencing and Bioinformatics, expressed in established primary human normal and cancer-associated fibroblasts (CAFs) from cancer and normal mucosa tissues from 9 colorectal cancer patients, and/or packaged in their derived exosomes. Differential representation and enrichment analyses based on these ncRNAs revealed a significant number of differences between the ncRNA content of exosomes and the expression patterns of the normal and cancer-associated fibroblast cells. ncRNA regulatory elements…
Classification of European and Mediterranean coastal dune vegetation
2018
Aims: Although many phytosociological studies have provided detailed local and regional descriptions of coastal dune vegetation, a unified classification of this vegetation in Europe and the Mediterranean Basin has been missing. Our aim is to produce a formalized classification of this vegetation and to identify the main factors driving its plant species composition at a continental scale. LocationAtlantic and Baltic coasts of Europe, Mediterranean Basin and the Black Sea region. - Methods: We compiled a database of 30,759 plots of coastal vegetation, which were resampled to reduce unbalanced sampling effort, obtaining a data set of 11,769 plots. We classified these plots with TWINSPAN, int…
Additional file 1: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Supplementary material and methods. (DOCX 28 kb)
Additional file 14 of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
: Table S2. Target genes for CAF-EXO over-distributed sncRNAs supported by FDR
Additional file 11: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in color…
2018
Table S1. sncRNAs distributed differently in CAF-EXO samples from in NF-EXO ones. Highly significant lncRNAs and sncRNAs (FDR
Additional file 8: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2019
Mini web site presenting a dynamic venn diagram showing the relationships between the results cellular or exosomal over represented in the two analyses performed between NF- and CAF- exosomes. Clicking on any intersected number, the web site opens a dialog summarizing the ncRNAs species that correspond to the intersection. (ZIP 354 kb)
Additional file 7: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2019
Mini web site presenting a dynamic venn diagram intersecting the relationships of significance from the assayed ncRNAs in the differential expression analyses performed between NF- and CAF- exosomes versus their respective cellular environments (i.e. NF-CELL versus NF-EXO and CAF-CELL versus CAF-EXO). Clicking on any intersected number, the web site opens a dialog summarizing the ncRNAs species that correspond to the intersection. (HTML 120 kb)
of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colorectal cancer
2019
of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colorectal cancer
Additional file 5: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Excel file with two documents summarizing the results obtained from the differential expression NF-CELL versus NF-EXO analyses for differentially distributed lncRNAs and sncRNAs. (XLSX 73 kb)
Additional file 12: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in color…
2018
Excel document with two documents summarizing the results for the significant sncRNAs in the differential expression analysis between NF-EXO and CA-FEXO samples and target predictions for those significant in CAF-EXO samples (positive logFCs). (XLSX 292 kb)
Additional file 3: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Excel document with the two count files used as input to EdgeR for differential expression analysis; one with the counts of reads of all samples mapped on the lncRNA references and another with the read counts of reads mapped on scnRNAs. (XLSX 221 kb)
Additional file 9: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Excel file with two documents summarizing the results obtained from the differential expression NF-CELL versus CAF-CELL analyses for differentially expressed lncRNAs and sncRNAs. (XLSX 10 kb)
Additional file 10: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in color…
2018
Excel document with two documents summarizing the results for the significant lncRNAs in the differential expression analysis between NF-EXO and CAF-EXO samples and target predictions for those significant in CAF-EXO samples (positive logFCs). (XLS 40 kb)
Additional file 4: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Figure S1. logFC-based MDS-plots (one for each type of lncRNA), where the first dimension corresponds to differences due to the type of sample (i.e. whether it is a normal cell, a tumor cell or an exosomal sample) and the second dimension corresponds to the differences between the samples themselves as biological replicates. The inferred dispersion and the Biological Coefficient of Variation (BCV) of all assayed samples for lncRNAs are 0.21201 and 0.4604, respectively, while the coefficients for sncRNA content are 0.25164 and 0.5016. These two coefficients reveal some interesting variation among samples. In this respect the multidimensional scaling (MDS) plots where the differences in ncRNA…
Additional file 6: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Excel file with two documents summarizing the results obtained from the differential expression CAF-CELL versus CAF-EXO analyses for differentially distributed lncRNAs and sncRNAs. (XLSX 60 kb)
Additional file 13 of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
: Multiple alignment of the 42 sncRNAs over represented in CAF-EXO samples. (FASTA 8 kb)
Additional file 2: of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
Absolute and average relative counts of reads mapped to each ncRNAs biotype per sample and fraction. (XLSX 15 kb)
Additional file 15 of Differential distribution and enrichment of non-coding RNAs in exosomes from normal and Cancer-associated fibroblasts in colore…
2018
: Figure S2. Heatmap with dendrogram showing the over-represented sncRNAs in CAF exosomes supported by FDRs below 1E-04 with the GO terms and metabolic pathways annotated to the predicted target genes summarized in Table 2. The number of target genes is used to color the breaks. If a sncRNA has no target gene assigned to a metabolic pathway (absence), the intersecting cell is colored white; if a ncRNA has one target gene assigned to a pathway, the cell is colored gray; and if more than two target genes are assigned to a pathway, it is colored black. The clustering was inferred by using the complete linkage with the Euclidean distance measure. (PNG 578 kb)