951a2f1ae953b7f284a8865ba7c6810823142b61
gperez2
  Fri Apr 22 09:53:56 2022 -0700
Updating ReMap track images, refs #28960

diff --git src/hg/makeDb/trackDb/human/reMap.html src/hg/makeDb/trackDb/human/reMap.html
index efedf17..6089397 100644
--- src/hg/makeDb/trackDb/human/reMap.html
+++ src/hg/makeDb/trackDb/human/reMap.html
@@ -3,34 +3,32 @@
 This track represents the <a href="http://remap.univ-amu.fr/"
 target="_blank">ReMap Atlas</a> of regulatory regions, which consists of a
 large-scale integrative analysis of all Public ChIP-seq data for transcriptional
 regulators from GEO, ArrayExpress, and ENCODE. 
 </p>
 
 <p>
 Below is a schematic diagram of the types of regulatory regions: 
 <ul>
 <li>ReMap 2022 Atlas (all peaks for each analyzed data set)</li> 
 <li>ReMap 2022 Non-redundant peaks (merged similar target)</li>
 <li>ReMap 2022 Cis Regulatory Modules</li>
 </ul>
 </p>
 
-<img src="http://remap.univ-amu.fr/storage/public/hubReMap2022/img/schema_datatype_remap.png"
-alt="Schematic diagram data types" style="display: block; margin-left: left;
-margin-right: auto; max-width:800px">
-<br>
+<img style='margin-left: 40px;' height=229 width=500
+src="../images/reMap_schema_datatype.png">
 
 <h2> Display Conventions and Configuration </h2>
 <ul>
 <li>
 Each transcription factor follows a specific RGB color.
 </li>
 <li>
 ChIP-seq peak summits are represented by vertical bars.
 </li>
 <li>
 Hsap: A data set is defined as a ChIP/Exo-seq experiment in a given
 GEO/ArrayExpress/ENCODE series (e.g. GSE41561), for a given TF (e.g. ESR1), in
 a particular biological condition (e.g. MCF-7).
 <br>Data sets are labeled with the concatenation of these three pieces of
 information (e.g. GSE41561.ESR1.MCF-7).
@@ -50,34 +48,32 @@
 This 4th release of ReMap (2022) presents the analysis of a total of 8,103 
 quality controlled ChIP-seq (n=7,895) and ChIP-exo (n=208) data sets from public
 sources (GEO, ArrayExpress, ENCODE). The ChIP-seq/exo data sets have been mapped
 to the GRCh38/hg38 human assembly. The data set is defined as a ChIP-seq 
 experiment in a given series (e.g. GSE46237), for a given TF (e.g. NR2C2), in a
 particular biological condition (i.e. cell line, tissue type, disease state, or
 experimental conditions; e.g. HELA). Data sets were labeled by concatenating
 these three pieces of information, such as GSE46237.NR2C2.HELA. 	
 </p>
 <p>Those merged analyses cover a total of 1,211 DNA-binding proteins
 (transcriptional regulators) such as a variety of transcription factors (TFs),
 transcription co-activators (TCFs), and chromatin-remodeling factors (CRFs) for
 182 million peaks. 
 </p>
 
-<img src="http://remap.univ-amu.fr/storage/public/hubReMap2022/img/fig2_hsap_2022-20.png"
-alt="Schematic diagram" style="display: block; margin-left: left; margin-right:
-auto; max-width:800px">
-<br>
+<img style='margin-left: 40px;' height=300 width=500
+src="../images/humanReMap.png">
 
 <h4>GEO & ArrayExpress</h4>
 Public ChIP-seq data sets were extracted from Gene Expression Omnibus (GEO) and
 ArrayExpress (AE) databases. For GEO, the query '('chip seq' OR 'chipseq' OR
 'chip sequencing') AND 'Genome binding/occupancy profiling by high throughput
 sequencing' AND 'homo sapiens'[organism] AND NOT 'ENCODE'[project]' was used to
 return a list of all potential data sets to analyze, which were then manually 
 assessed for further analyses. Data sets involving polymerases (i.e. Pol2 and
 Pol3), and some mutated or fused TFs (e.g. KAP1 N/C terminal mutation, GSE27929)
 were excluded.
 
 <h4>ENCODE</h4>
 Available ENCODE ChIP-seq data sets for transcriptional regulators from the
 www.encodeproject.org portal were processed with the standardized ReMap pipeline.
 The list of ENCODE data was retrieved as FASTQ files from the ENCODE portal