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The small network is composed of Klf4 (which is also a focus of highlighting by ExprEssence, due to its strong down-regulation) and Arid3a, which is the protein linked to Klf4 that changes most significantly.
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The protein links we estimate to be broken between a protein containing a DA-SNP and its immediate neighbors are shown in Figure 3A and 3B for focal adhesion and natural killer cell mediated immunity.
We have used GO molecular function annotations of the proteins linked to each fragment for functional descriptions of fragment clusters (Figure 1E).
The proteins linked to apoptosis or cell survival are indicated in Table 3.
Another popular database, REACTOME, also provides the expressions of the proteins linked with a signaling pathway across different tissues.
Thus, we observed a significantly higher number of PP1 docking motifs within the proteins linked with non-syndromic hereditary deafness.
The proteins linked to the chromatin were extracted as described in Hervouet et al. Protein concentration was determined using Bradford assay (Bio-Rad, Hercules, CA, USA).
It is reported that CPPs enter cells by an endocytic mechanism, and the proteins linked with the CPP tend to rapidly concentrate inside the endocytic organelles.
In both experiments with the MIPS network, we filtered candidates by examining only a subset of the proteins linked to the elements in the query set by a path of no more than two proteins.
The proteins linked to the radioresistant trait of the NPC cells have been identified through proteomics in two independent studies using a radioresistant subclone cell line (CNE2-IR) derived from NPC cell line CNE2 [ 60, 61].
Here is the full WHAT_CHECK report on this protein (linked from the WHAT_CHECK site).
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