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Before comparing the differential expression of genes in response to Cd treatment, normalized gene expression levels were obtained by normalizing the number of raw clean tags in each library to the number of transcripts per million clean tags (TPM).
The probability b ij is finally obtained by normalizing the number of sample points in a pixel n ij to the total number of sample points on all projections for a given j, i.e. ( {sum}_{k=0}^{K-1}{N}_{mathrm{grid},j,k}^2 ) where the sum goes over the all K projections {b}_{ij}=frac{n_{ij}}{sum_{k=0}^{K-1}{N}_{mathrm{grid},j,k}^2}.
With the similarity matrix, by normalizing the number of markers into percent and calculating the level of shared markers as a percentage of the total markers, these values can be shown graphically and compared between species (Fig. 3).
Chemotactic index was calculated by normalizing the number of cells that migrated under basal conditions to 1. Data analysis was performed using GraphPad Prism 5 software (GraphPad Software, Inc., San Diego, CA).
Since shorter protein sequences have a large fraction of residue pairs in contact with each other (Figure S3B), we repeated the analysis adjusting for sequence length by normalizing the number of top scoring site pairs chosen for each protein family by the length of the protein sequence (Figure S6).
The ratio of cell growth was calculated by normalizing the number of experimental cells to that of control cells.
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The relative rates of the corresponding events of each lineage were computed by normalizing the numbers of events using inferred branch lengths.
To compare differences in U2AF65 binding between conditions, we corrected for changes in transcript levels by normalizing the numbers of crosslink events.
The spot density was obtained by normalizing the total number of analyzed particles to the axonal area measured via HRP.
We also calculated the publication output on sepsis by normalizing the total number of articles to the gross domestic product (GDP) per capita of the included countries.
Colony formation units (CFU) were calculated by normalizing the colony number to the value obtained with pEPito-hCMV/EF1-EGFP-IRES-BSD-ΔSMAR as recently described [ 17].
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