286 try: --> 287 df_annotated_features, rccs, rankings, genes, avg2stdrcc = module2features_func( 288 db, module, motif_annotations, weighted_recovery=weighted_recovery 289 ) 290 except MemoryError: 291 LOGGER.error( 292 'Unable to process "{}" on database "{}" because ran out of ...
The motif rankings version used was human hg38 refseq-r80 for 500 bp upstream and 100 bp downstream the transcription start site. The motif-to-TF annotation version used was human v9. Gene-disease associations To generate a list of genes associated with disease, we used the DisGeNET database...
利用DrugnomeAI[29]对关键易感基因可药性进行预测,当DrugnomeAI gene rankings的percentile score>60时,认为关键易感基因具有潜在可药性。以“过敏性鼻炎/变应性鼻炎+靶点名”为关键词,利用PubMed(https://pubmed.ncbi.nlm.nih.gov/)和中国知网(https://www.cnki.net/)查询是否有论文直接支撑关键易感基因与AR...
(ctxcore>= 0.2), which allow uses recent versions of pyarrow (>=8.0.0) instead of very old ones (<0.17). Databases in the new format can be downloaded fromhttps://resources.aertslab.org/cistarget/databases/and end with*.genes_vs_motifs.rankings.featheror*.genes_vs_tracks.rankings....
To assess the effect of clustering in the motif collection, we also benchmarked SCENIC using the non-clustered and the clustered databases at the same time, obtaining similar results. For each collection, we generated two gene–motif rankings (10 kb around the TSS or 500 bp upstream the...
More generally, the rankings can be combined to detect interactions between any disjoint sets of SNPs, such as biological pathways or regulatory regions. Let p′ be the total number of genes in the disease map, and let us denote by Gi′ the set of SNPs mapped to gene i′ . The ...
The gene rankings for females and males can be found in Additional file 3: Table S3. The most highly ranked genes correspond with regions of the network that are inherently connected to mtDNA-sensitive genes and are not necessarily the DE genes themselves. This ap- proach is likely to be ...
Scatterplot comparing Lisa TR rankings with combined P-values predicted to regulate female- and male-biased genes. Each TR is represented by a point. The combined − log10(P-value) is plotted for each TR based on female-biased and male-biased gene sets which are sex-biased in the same...
See also the list of genes and their rankings in Table S4. (E–G) qPCR analysis of H3K9bhb, H3K4me3, and H3K9ac ChIP products from mouse livers either fed normally or fasted for 48 hr. Data are represented as means ± SEM (n = 3). NS p > 0.05, ∗p < 0.05, ∗∗p < ...
For comparison, we also generated sgRNA-UMI-informed fitness estimates and confidence intervals using a frequentist methodology based on a ratio statistic and the Delta method (Supplementary Methods1.4). While Bayesian and frequentist methodologies generated broadly similar rankings of guide fitness in sing...