Journal: BMC Genomics

Article Title: The transcriptome of the NZ endemic sea urchin Kina ( Evechinus chloroticus )

doi: 10.1186/1471-2164-15-45

Figure Lengend Snippet: GO annotations. Top 10 represented GO terms for each of the GO categories; Molecular Function, Biological Process and Cellular Component. GO terms annotated by protein similarity to the NCBI non-redundant database and from InterProScan results.

Article Snippet: Additional GO terms could be retrieved from the InterProScan results and merged with existing GO annotations, 11,478 transcripts had GO terms associated with InterPro results.

Techniques:

Journal: BMC Genomics

Article Title: The transcriptome of the NZ endemic sea urchin Kina ( Evechinus chloroticus )

doi: 10.1186/1471-2164-15-45

Figure Lengend Snippet: InterPro annotations. Top 10 represented InterPro terms from the InterProScan annotations.

Article Snippet: Additional GO terms could be retrieved from the InterProScan results and merged with existing GO annotations, 11,478 transcripts had GO terms associated with InterPro results.

Techniques:

Journal: Cell Reports

Article Title: A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells

doi: 10.1016/j.celrep.2017.04.062

Figure Lengend Snippet: Whole-Cell and PM Proteins Co-regulated by EBV, CMV, and KSHV K5 (A) Overlap between EBV and CMV WCL data. 7,490 proteins were quantified in either CMV experiment WCL1 or WCL2 or both ( Weekes et al., 2014 ). 6,389 of these proteins were additionally quantified in EBV experiments WCL1–3. From this overlap, 1,083 proteins were downregulated either by EBV or CMV, of which 43 were downregulated by both viruses. This initial “non-stringent” filtering included proteins downregulated in (1) all of experiments WCL1–3, (2) any combination of two of three experiments, but not quantified in the third, and (3) any one of three experiments, but not quantified in the other two. Using “stringent” filtering, we identified a subset of ten proteins downregulated in all three EBV and both CMV experiments, that were additionally downregulated at least 2-fold more than the P3HR1 parental control, to exclude non-specific effects of tamoxifen treatment ( Figure 2 and ). Of the 19 proteins upregulated by both viruses, only one (APOE) met our stringent criteria. (B) DAVID analysis identified eight of ten stringently filtered proteins functioning in poly(A) RNA binding (p < 0.001), of which six are known to interact (STRING database). Blue lines represent experimental evidence for physical binding, purple for catalysis, and black for reaction. Gray bars indicate evidence for co-expression. (C) Example plots of two of the ten proteins GNL3 and TXNIP. Left: EBV experiments WCL 1–3. Right: CMV Experiment WCL2. (D) Analysis of co-regulated PM proteins. We used similar non-stringent filter as detailed in (A), comparing EBV experiment PM1 with HCMV experiments PM1 and PM2. Stringent filtering excluded non-specific effects of tamoxifen treatment only, as there was no second temporal replicate for the EBV PM experiment. (E) 12/16 downregulated proteins met our stringent criteria, of which the top four listed functioned in synapse organization (p < 0.05). 46/48 upregulated proteins met our stringent criteria. (F) Temporal proteomic analysis of NLGN4X and PCDHGC3. Left: EBV experiments WCL 1–3. Right: CMV experiment WCL 2. (G) Coregulation of PM proteins by EBV and the KSHV K5 gene. Nine proteins met the stringent filter (D), of which three were additionally downregulated by CMV (green text) (E).

Article Snippet: DAVID software suggested that this group was particularly enriched in proteins with Interpro categories that included “Unfolded protein binding,” “Endoplasmic reticulum (ER) lumen,” “chaperone,” suggesting increased ER stress.

Techniques: Control, RNA Binding Assay, Binding Assay, Expressing