Vel values are assigned to more specific child terms.

PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/7765207Unless Vel values are assigned to more specific child terms. Unless PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/7765207 more than one parent is assigned, GO level can be considered as a constant value for each term. As GO level values refer to the position of the enriched terms in the GO hierarchy tree, they can define the specificity or granularity of a given GO term and thus are a valuable parameter for terms prioritization and for inferring biological meaning from GO 1-(Cyclopropylsulfonyl)-1,4-diazepane enrichment analysis [39]. To determine the position of each of the enriched GO terms in the DAG structure of the gene ontology hierarchy, we performed GO Biological Process (BP) enrichment at GO levels between 20 and 3, using STEM. This led to multiple lists of enriched and overlapping GO terms at each level of GO hierarchy. Using this approach, a single GO level was assigned to every GO term. 2-Bromo-4-fluoro-5-methylbenzoic acid Figure 4B depicts the distribution of all 649 and 329 GO terms obtained at p 0.001 and p 0.0001 cut offs, respectively, against theirChamankhah et al. BMC Genomics 2013, 14:583 http://www.biomedcentral.com/1471-2164/14/Page 9 ofAAverage Fold ChangeBProfile275.5 genes assigned, 45.8 genes expected p-value = 2.1 E-Average Fold PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/10714611 ChangeProfile50 genes assigned, 24.8 genes expected p-value = 5.1 E-0 0 7 14 21 28 35 42 490 0 7 14 21 28 35 42 49Days Post-InjuryDays Post-InjuryCAverage Fold ChangeD52.0 genes assigned, 33.2 genes expected p-value = 1.4 E-Average Fold ChangeProfile-0.Profile179.0 genes assigned, 38.4 genes expected p-value = 5.7 E--1.-2.0 0 7 14 21 28 35 42 49-3.5 0 7 14 21 28 35 42 49Days Post-InjuryDays Post-InjuryEAverage Fold Change-0.F186.0 genes assigned, 43.7 genes expected p-value = 1.5 E-Average Fold ChangeProfile4 3-1.-2.Profile 44,1566.5 genes assigned, 45.2 genes expected p-value = 0.0 7 14 21 28 35 42 49-3.5 0 7 14 21 28 35 42 49Days Post-InjuryDays Post-InjuryGAverage Fold ChangeAverage Fold ChangeProfile68.5 genes assigned, 41.3 genes expected p-value = 4.2 E-H-0.Profile364 genes assigned, 42.7 genes expected p-value = 1.8 E--1.-2.-3.0 0 7 14 21 28 35 42 49-4.5 0 7 14 21 28 35 42 49Days Post-InjuryDays Post-InjuryFigure 3 Distinct Significant Expression Profiles Clustered by STEM. A-H. Average fold change values for the genes in each cluster were plotted against the real time scale of the time-points post-injury. Error bars denote the standard deviation of the mean. Three classes of expression profiles are observed. Class I profiles (A-C) display an "up-down" pattern with the peak of up-regulation in 24 hours (profiles 45, 46 and 48) post-injury. The up-regulation is followed by decline of transcript levels, either sharply back to normal values (profiles 45 and 48) or gradually to higher than control values (profiles 46). Class II profiles (1 and 0) are quite similar to each other as they display down-regulations of many genes on day 1, which stay at lower than normal levels even at 8 weeks post-injury. Class III profiles (E-H) represent fluctuating profiles and are subdivided into two clusters. Cluster I (Profiles 44 and 41) is marked by an early increase in gene expression by day 1 followed by sudden decline in transcript level at day 3. In profile 44, this transient change in transcription level is followed by an escalating condition whereby the same transcripts are again up-regulated by day 7 and stay at higher than control values until 8 weeks post-injury. In cluster II (profile 6), a reverse phenomenon is observed, where the early event is a sharp decrease in transcript level and a follow up fluctuation pattern.