Expression analysis of G Protein-Coupled Receptors in mouse macrophages-2

over a timecourse of 0, 2, 6, and 24 h, and 0, 1 and 7 h, respectively. Data points show gene expression relative to untreated control for each cell population (0 h).<p><b>Copyright information:</b></p><p>Taken from "Expression analysis of G Protein-Coupled Receptors in mouse macrophages"</p><p>http://www.immunome-research.com/content/4/1/5</p><p>Immunome Research 2008;4():5-5.</p><p>Published online 29 Apr 2008</p><p>PMCID:PMC2394514.</p><p></p

Expression analysis of G Protein-Coupled Receptors in mouse macrophages-1

Of 91 murine cell types and tissues. Data points show normalised values and similar cell types are grouped according to bar colour; blue indicates primary macrophage cell types, purple indicates bone-related cell types, red indicates other immune cell types, green indicates stem cell populations, orange indicates whole tissue samples, yellow indicates neuronal and retinal cell types and pink indicates cell lines. Additional file gives details of the 91 cell types and tissues profiled.<p><b>Copyright information:</b></p><p>Taken from "Expression analysis of G Protein-Coupled Receptors in mouse macrophages"</p><p>http://www.immunome-research.com/content/4/1/5</p><p>Immunome Research 2008;4():5-5.</p><p>Published online 29 Apr 2008</p><p>PMCID:PMC2394514.</p><p></p

Expression analysis of G Protein-Coupled Receptors in mouse macrophages-0

Of 91 murine cell types and tissues. Data points show normalised values and similar cell types are grouped according to bar colour; blue indicates primary macrophage cell types, purple indicates bone-related cell types, red indicates other immune cell types, green indicates stem cell populations, orange indicates whole tissue samples, yellow indicates neuronal and retinal cell types and pink indicates cell lines. Additional file gives details of the 91 cell types and tissues profiled.<p><b>Copyright information:</b></p><p>Taken from "Expression analysis of G Protein-Coupled Receptors in mouse macrophages"</p><p>http://www.immunome-research.com/content/4/1/5</p><p>Immunome Research 2008;4():5-5.</p><p>Published online 29 Apr 2008</p><p>PMCID:PMC2394514.</p><p></p

Distribution of Densities of Selected PEs in Promoters of the Four TSS Types in Mouse

<div><p>The density of PEs is calculated from the region covering [−100, +100] relative to the TSS. Density is determined for bins of length 50 bp and shifted by 10 bp. In total, there are 17 bins. The vertical axis shows the percentage of TSSs of the considered type that contain the PE.</p> <p>(A) Distribution of selected PEs that prefer GC-rich (left) and AT-rich (right) domains in type B (above) and type C (below) TSS groups. Bin number 9 is centered around the TSS. It can be seen that groups of PEs change significantly in their concentrations in transition from upstream to downstream regions and characterize two distinct TSS types (B and C).</p> <p>(B) Distribution of selected PEs across all four TSS types. Blue, green, red, and light blue correspond to distributions characterized by type A, B, C, and D TSSs. The first five PEs are those that prefer GC-rich regions, and the last seven PEs prefer AT-rich regions (the plus or minus sign in front of the TFBS symbol denotes the strand where the TFBS is found).</p></div

Sequence Logos

<div><p>(A) Sequence logos for Inr in human (left) and mouse (right) obtained using [−5, +5] segments relative to TSS locations. There is an evident bias in the nucleotide composition surrounding the TSS that effectively determines different Inr elements.</p> <p>(B) Sequence logos for segments [−35, +20] relative to TSS locations. Strong similarity exists between human (left) and mouse (right) in TSS type A, while that similarity is considerably reduced for the other TSS types.</p></div

Transcription Initiation Domains for Mouse and Human

<p>Distribution of mouse (red) TSSs overlapped by human (blue) TSSs based on (A) C + G content, (B) A + G content, and (C) T + G content. Nucleotide content is determined for upstream [−100, −1] and downstream [+1, +100] regions relative to the TSS. The distribution of TSS locations is more or less random when viewed in terms of A + G content (B) or T + G content (C). Strong polarization of distributions is evident only in the G + C case (A).</p

Distribution of Selected Groups of PEs That Are Highly Enriched (at Least 3-Fold) Upstream or Downstream of the TSS

<p>The upstream region considered covers [−100, −1], while the downstream region covers [+1, +100] relative to the TSS. In all TSS types, the upstream region contains significantly more enriched PEs than the downstream region.</p

Distribution of TSSs for Transcripts Related to Immune Response through GO:0006955

<p>There are 1.58-, 4.85-, and 3.35-fold more transcripts having TSS types B, C, and D than one would expect based on the proportion of transcripts in these groups in our reference mouse data. Enrichment is statistically significant for types C and D based on Bonferroni corrected <i>p</i>-values obtained by the right-sided Fisher's exact test (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020054#pgen-0020054-t005" target="_blank">Table 5</a>).</p

Distribution of Mononucleotides in Mouse Promoters in the Region Surrounding the TSS

<p>The nucleotides adenine, cytosine, guanine, and thymine are represented by blue, green, red, and light blue, respectively. The TSS types that are GC-poor upstream (C and D) show very characteristic enrichment in adenine and thymine nucleotides around [−35, −20], suggesting a potential dominant influence of TATA box and similar AT-rich elements in transcription initiation in these types. In type B and A TSSs, this influence does not seem to be dominant, but the presence of such elements is suggested by a significant reduction of the GC content in the [−35, −20] region. In principle, one could attempt to link the types of AT-rich upstream elements with initiating dinucleotides characteristic of different TSS types.</p

Annotation Pipelines for Transcript Description and for GO Terms

<div><p>(A) Pipeline for transcript description. Query sequences falling into categories (black boxes) 1–3 were assigned the description of the matched target sequence DNA entry in MGI symbols, and synonyms were also transferred to our annotation database. Queries falling into categories 4–10 were assigned a transcript description corresponding to the matched protein name. For query sequences falling into category 5 or 6, the keyword “homolog” was appended to the matching protein name. Sequences assigned to category 7 or 8 were denoted with the prefix “similar to” attached to the target sequence name. The prefix “weakly similar” was used to identify sequences assigned to category 9 or 10. For all sequences in categories 5–10, the name of the organism corresponding to the matched protein was appended to the assigned transcript description. If a query was assigned to category 14, its transcript description was “hypothetical [InterPro domain name] containing protein.” Query sequences assigned to category 17 and 19 were annotated as “hypothetical protein” and “unclassifiable,” respectively. Query sequences grouped into category N1 or N2 were assigned the description of the matched target ncRNA entry. For query sequences falling into category N2, the keyword “homolog of” was appended to the matching ncRNA name.</p> <p>(B) Pipeline for GO terms.</p> <p>DB, database.</p></div