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Figure 1. The workflow of Cistrome-GO

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1 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) 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 ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz332, The content of this slide may be subject to copyright: please see the slide notes for details.

2 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, , , 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, 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 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) 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 ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz332, The content of this slide may be subject to copyright: please see the slide notes for details.

3 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) 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 ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz332, The content of this slide may be subject to copyright: please see the slide notes for details.

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