1 to 10 of 15 Results
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Annotated list of species used in this study", https://doi.org/10.15454/IIAQOW, Portail Data INRAE, V1
Annotated list of the 63 species used in the Orthofinder comparative analysis of nematodes (61 species) and two tardigrade species as out-groups. Description: Lines 1-64, definition of columns - Abbrev Species: abbreviated species name. Species identifiers used in all the Orthofi... |
Oct 19, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Grynberg, Priscila; Danchin, Etienne, 2020, "Gene Ontology enrichment in PPN-specific and horizontally acquired proteins", https://doi.org/10.15454/8NZABA, Portail Data INRAE, V3, UNF:6:yJukDnmw5qngLgeT3hhznw== [fileUNF]
We used a hypergeometric test within the FUNC program (Prüfer et al., 2007) to determine whether certain GO terms assigned via InterproScan annotation were significantly enriched in M. incognita : - PPN-specific proteins - PPN-specific putative secreted proteins (PSP) - PPN-speci... |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Global statistics of the orthofinder analysis", https://doi.org/10.15454/ZGUP7N, Portail Data INRAE, V1
General statistics of the orhofinder analysis on the 63 species (including 61 nematodes). Number of orthogroups, of genes in orthogroups etc... |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne; Rancurel, Corinne, 2020, "Horizontal gene transfer candidates in M. incognita", https://doi.org/10.15454/W6SWZH, Portail Data INRAE, V1, UNF:6:wuWOjB++Puk5yJOSrDfxWw== [fileUNF]
Analysis of horizontal gene transfer (HGT) candidates on the M. incognita predicted proteins from (Blanc-Mathieu et al. 2017), using Alienness (Rancurel et al. 2017) on a Diamond search against the NCBI's nr library. The following parameters were used in Alienness Taxonomic group... |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "M. incognita candidate effector proteins", https://doi.org/10.15454/CSTXU2, Portail Data INRAE, V1
Accession numbers of M. incognita candidate effectors. These proteins are predicted to be secreted based on the presence of a signal peptide for secretion and absence of transmembrane domains. Furthermore at least one motif known to be enriched in effector proteins is present in... |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "M. incognita predicted secreted proteins", https://doi.org/10.15454/JCYZDI, Portail Data INRAE, V1
To identify putative secreted proteins in the M. incognita protein set (Blanc-Mathieu et al. 2017), we searched for predicted signal peptides (SP) for secretion using SignalP v4 (Petersen, Brunak, von Heijne, & Nielsen, 2011). This program improves the differentiation between tra... |
Jul 3, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne; Da Rocha, Martine, 2020, "M. incognita protein-coding genes expression patterns", https://doi.org/10.15454/YM2DHE, Portail Data INRAE, V1
M. incognita protein-coding genes expression values across 4 life stages in triplicates. Life stages are as follows: - W: eggs - J2: pre-parasitic infective juveniles - J3: infective juveniles (mic of late J2, J3 and J4) - Fem: adult female Two tables are given, one with the raw... |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "M. incongnita proteins specific to plant-parasitic nemaotdes", https://doi.org/10.15454/I9MWRS, Portail Data INRAE, V1
Accession numbers of M. incognita predicted proteins having predicted homologs only in other plant-parasitic nematodes (PPN) or being M. incognita-specific. |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "Meloidogyne incognita Interproscan annotation", https://doi.org/10.15454/9BFFKG, Portail Data INRAE, V1
Interproscan annotation on the 43,718 predicted proteins in the genome of the root-knot nematode Meloidogyne incognita (Blanc-Mathieu et al. 2017, PLoS Genetics). vesrion used: interproscan-5.29-68.0 options used: -dp Disables use of the precalculated match lookup service = all m... |
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins", https://doi.org/10.15454/LMY6LV, Portail Data INRAE, V1
MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins M. incognita proteins with at least one of the 4 motifs identified as enriched in the known effector proteins as described in (Vens, Rosso, Danchin, Bioinformatics, 2011) |