To further explore gene expression similarities corresponding to development stage, we applied a correspondence analysis to the complete dataset and to a group-combined expression matrix (samples within a development group was combined using a trimmed mean) [ 23].
Performing multiple core flooding tests and analyzing the data, we define the range of rock properties and flow conditions corresponding to development of the situ formation damage (self-colmatation).
We interpret this region as corresponding to development and alignment of a β-sheet network as shear forces bring the N- and C- termini sections of the proteins into close proximity, as well as increasing alignment of the coiled coil regions.
Conversely, the activity of metalloprotease MMP-2 increased at later time points (since day 7) corresponding to development of fibrosis [ 36].
Heat maps corresponding to development and stress clustering solutions are provided in section 1C of additional file 1. Genes clustered together with respect to both Development and Stress datasets Genes are ordered from least to most stress-responsive (according to d).
To address the proportion of correspondence between the respondents' results and the ideal case (i.e. the codes corresponding to development of a TMM or taking practical patient safety actions) several analyses were carried out.
Concretely, several GO categories related to metabolic processes, as well as some involved in specific responses, are particularly overrepresented in short loci (<80 kb), while GO categories corresponding to development, morphogenesis, regulation and signaling are significantly overrepresented in loci longer than 120 kb (Table 1).
For the following gene categories corresponding to development and biogenesis (15 in early and 19 in middle), and transport (12 in early and 38 in middle), the number of transcribed genes was higher in the middle stage when compared to the early stage.
The network is weighted with differential gene expression corresponding to adenoma development, tumor growth, and cancer progression.
We selected four time-points corresponding to the development of pigmentation during seed growth and maturation for PI 84970 (black seed coats) and PI 567115 B (brown seed coats) (Additional File 4).
