Figure 1. The workflow of Cistrome-GO

Slides:

Advertisements

Similar presentations

J Exp Bot. 2017;68(17): doi: /jxb/erx352

Advertisements

Figure 3: MetaLIMS sample input.

Figure 2. The graphic integration of CNAs with altered expression genes in lung AD and SCC. The red lines represent the amplification regions for CNA and.

From: Introducing the PRIDE Archive RESTful web services

Figure 1. The flow chart illustrates the construction process of anti-CRISPRdb, and the information that users can obtain from anti-CRISPRdb. From: Anti-CRISPRdb:

Figure 2. Workflow of MethMotif Batch Query

Figure 3. Schematic representation of co-expression networks for BipA, SidD, and Erg11 encoding genes. Genes are represented by circles, with positive.

Figure 1: Necrobiosis lipoidica: Yellow-brown skin lesions with indurated borders located on both lower legs. Figure 1: Necrobiosis lipoidica: Yellow-brown.

Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway ... Figure 1. (A) The VEGF promoter.

Figure 1. Sgs1 binds to RPA-coated ssDNA

Figure 1. Circular taxonomy tree based on the species that were sequenced in our study. Unless provided in the caption above, the following copyright applies.

Figure 1. An example of a thioviridamide-like molecule, thioalbamide, and inset, a proposed biochemical route to ... Figure 1. An example of a thioviridamide-like.

Figure 1. Biased distribution of different SV classes

Figure 1. Overview of the workflow of NetworkAnalyst 3.0.

Figure 1 The study area within Vienna Zoo is outlined in red

Figure 4. (A) Venn diagram showing the overlap of peaks differentially changed in DHT as compared to NT with peaks ... Figure 4. (A) Venn diagram showing.

FIGURE 1 Histological diagnoses divided into 8-year time frames (n = 1208). Unless provided in the caption above, the following copyright applies to the.

FIGURE 1 The effect of daprodustat on hemoglobin (Hgb) levels

Figure 2. Ectopic expression of PLZF modulates H3K27ac at enhancer regions in myeloid cells. (A) Box plots showing ... Figure 2. Ectopic expression of.

Figure 1. BRCA1-associated R-Loop accumulation at a non-coding region upstream of ESR1 locus. (A) Alignment of DRIP-seq ... Figure 1. BRCA1-associated.

FIGURE 2 Responses to the question: regarding vasoactive drugs, does your centre use the following frequently, rarely ... FIGURE 2 Responses to the question:

Figure 1. Designing a cell-specific Cas-ON switch based on miRNA-regulated anti-CRISPR genes. (A) Schematic of the ... Figure 1. Designing a cell-specific.

Figure 1. Schematic illustration of CSN and NDM construction and our statistic model. (A) CSN and NDM construction. (i) ... Figure 1. Schematic illustration.

Figure 1. Ratios of observed to expected numbers of exon boundaries aligning to boundaries of domain and disorder ... Figure 1. Ratios of observed to expected.

Figure 1. autoMLST workflow depicting placement and de novo mode

Figure 1. The 12 species in this study and details of the improved G4-seq method. (A) Phylogenetic representation of ... Figure 1. The 12 species in this.

Figure 1. Comparison of weighted estimates of diarrhoea prevalence in children under five by country between PMA Figure 1. Comparison of weighted.

Figure 1. Nanopore methylation calls are consistent with expected results and established technologies. (A) Metaplot of ... Figure 1. Nanopore methylation.

Fig. 1 Kaplan-Meier plot of cumulative incidence of cancer onset following dermatomyositis diagnosis stratified ... Anti-TIF1-Ab: anti-transcriptional.

Figure 1. Chemical structures of DNA and tc-DNA

Point estimates with ... Point estimates with 95% CI. HR: hip replacement; KR: knee replacement. Unless provided in the caption above, the following copyright.

FIGURE 1 Participant flow diagram. Exercise Counseling Clinic (ECC).

Graph 1. The number of homicide cases per year discussing neuro-evidence. Unless provided in the caption above, the following copyright applies to the.

Figure 1. Analysis of human TRIM5α protein with Blast-Search and PhyML+SMS ‘One click’ workflow. (A) NGPhylogeny.fr ... Figure 1. Analysis of human TRIM5α.

Figure 1. Mean concentration–time profiles of ascending doses of ivermectin in (a) PSAC and (b) SAC. Weight-dependent ... Figure 1. Mean concentration–time.

Figure 1 Nelson-Aalen estimates of the cumulative incidence rates for patients on versus off IST. ON = optic neuritis; ... Figure 1 Nelson-Aalen estimates.

FIGURE 1 Malta: a plate-style food guide

Figure 1. A, Crude incidence rates per 100 person-years of follow-up and 95% confidence intervals for each solid organ ... Figure 1. A, Crude incidence.

FIGURE 1 Study consort diagram

Fig. 2 Case 2. Levels of serum creatinine and anti-GBM antibodies before and during treatment with cyclophosphamide, ... Fig. 2 Case 2. Levels of serum.

Figure 1. Illustration of DGR systems and their prediction using myDGR

Figure 1. The pipeline of Aggrescan3D 2.0 server.

Figure 1. Summary of experimental conditions and data normalization

Figure 1. Prediction result for birch pollen allergen Bet v 1 (PDB: 1bv1), as obtained by comparison to the cherry ... Figure 1. Prediction result for.

Figure 1. Using Voronoi tessellation to define contacts

Fig. 1. iS-CellR pipeline overview

Figure 4. RLS spectra of (A) TMPipEOPP and (B) OMHEPzEOPP in the presence of different concentrations of KRAS. The RLS ... Figure 4. RLS spectra of (A)

Figure 1. PaintOmics 3 workflow diagram

Figure 1. Schematic diagram of solar energy and coal-fired power generation system. Unless provided in the caption above, the following copyright applies.

Figure 1. Uncertainty reduction, value creation, and appropriation in two case studies. Unless provided in the caption above, the following copyright applies.

Figure 1. The configuration menu allows the user to choose among the main visualization/processing options of the ... Figure 1. The configuration menu.

Figure 1. (A) Architecture of Doc2Hpo. (B) Interactive user interface

Figure 1. MERMAID web server interface (Start page, Parameter page): MERMAID provides two ways to submit a protein ... Figure 1. MERMAID web server interface.

Figure 1. Yvis platform overview

Figure 1. The framework of NetGO with seven steps

Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein ... Figure 1. Workflow of the HawkDock.

Figure 1. Overview of features that can be assessed in a single RegulationSpotter VCF analysis run. Depending upon a ... Figure 1. Overview of features.

Figure 1 Patient disposition

Figure 1. Workflow of the analysis to estimate the number of true human miRNAs. Samples containing NGS data were ... Figure 1. Workflow of the analysis.

Figure 1 Distribution of WCD use days in WEARIT-II

Figure 1. SQL schema used by RetroRules

Figure 1 Correlation between en face Oil-Red O staining and aortic root lesion size vs. plasma cholesterol and ... Figure 1 Correlation between en face.

Figure 1. Excess cost of methicillin-resistant Staphylococcus aureus (MRSA) compared with methicillin-susceptible S. ... Figure 1. Excess cost of methicillin-resistant.

Figure 1 Genetic results. No case had more than one diagnostic result

Figure 1. Prevalence of parasitic infection and anemia among the children. Unless provided in the caption above, the following copyright applies to the.

Figure 1. Optimization of the variant calling algorithm, ADIScan1, by tangential conversion of read depth ratios ... Figure 1. Optimization of the variant.

Figure 1. GWAS Catalog associations for coronary artery disease plotted across all chromosomes. Associations added ... Figure 1. GWAS Catalog associations.

Figure 1 Mechanisms of mitral regurgitation.

Fig. 1. Examples of plots of NanoPlot and NanoComp

Figure 1. (A) Overview of ENPD including data source, data processing and features. Transcriptomes from TSA, genomes ... Figure 1. (A) Overview of ENPD.

Presentation transcript:

Figure 1. The workflow of Cistrome-GO Figure 1. The workflow of Cistrome-GO. (A) Schema of RP score calculation for gene g. Two peaks are located near to ... Figure 1. The workflow of Cistrome-GO. (A) Schema of RP score calculation for gene g. Two peaks are located near to gene g, with peak to TSS genomic distances of d<sub>1</sub> and d<sub>2</sub>. All k ChIP-seq peaks near the TSS of gene g are used in the RP score calculation (k = 2 in this figure). The pink area represents the decay function used in the RP score calculation. The parameter d<sub>0</sub> is the decay distance of the peak weighting function. (B) The ensemble mode workflow. If the user uploads both TF ChIP-seq peak and DGE analysis files, Cistrome-GO will perform an ensemble mode analysis based on the integration of the two types of data with the following three steps. Step 1: calculation of the adjusted RP score. Step 2: integration with differential expression data by rank product. Step 3: GO and pathway analysis based on gene ranking. Given a GO or KEGG term j, the gene ranking (with high ranking genes represented in bright pink) is translated into a series of 1s or 0s, which indicate the presence or absence of the ranked genes in the jth term. The mHG test is applied to this series to assess whether the 1s tend occur near the top of the ranked gene list. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz332, https://doi.org/10.1093/nar/gkz332 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. The performance of Cistrome-GO in solo mode Figure 2. The performance of Cistrome-GO in solo mode. (A) Evaluation of the performance between Cistrome-GO and other ... Figure 2. The performance of Cistrome-GO in solo mode. (A) Evaluation of the performance between Cistrome-GO and other web servers (including GREAT, ChIP-Enrich and Enrichr) on 256 TF ChIP-seq datasets. For each web server, the most significant 5000, 10 000, 15 000, 20 000 and all ChIP-seq peaks were used in the evaluation separately. The MSS score quantifies the similarity between the web server predictions and the standard set of GO terms for each TF. (B) The percentage of the most significant E2F1 ChIP-seq peaks (top 2000, 5000, 10 000 and all peaks separately; ranked by −log<sub>10</sub>(P-value)) are close (<1 kb) to TSS. (C) The top 10 enriched BP terms for 10 000 E2F1 ChIP-seq peaks using 1 kb as the decay distance. The BP terms indicated by red arrows are those relevant to cell-cycle functions. The color gradient represents the gene number in each GO term. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz332, https://doi.org/10.1093/nar/gkz332 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. The performance of Cistrome-GO in ensemble mode, with STAT3 ChIP-seq and STAT3 knock-down DGE data as input. ... Figure 3. The performance of Cistrome-GO in ensemble mode, with STAT3 ChIP-seq and STAT3 knock-down DGE data as input. (A) The top 10 enriched BP terms in the ensemble mode. The BP terms indicated by red arrows are those relevant to STAT3’s reported functions. (B) The top 10 enriched BP terms for STAT3 in solo mode. The BP terms indicated by red arrows are those relevant to STAT3’s reported functions. The color gradient represents the gene number in each GO term. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz332, https://doi.org/10.1093/nar/gkz332 The content of this slide may be subject to copyright: please see the slide notes for details.