Defining Ubiquitous Chromatin Opening Elements (UCOE®) molecular mechanisms of action for expediting their biotechnological applications

Tables_A1_A2_A3.xlsx

Table A1: List of all proteins extracted from ReMAP, occupying A2UCOE and RPS3 region, ordered by joint ranking.  Table contains number of sites from combined ChIP experiments separately for both UCOEs and combined. List 1. 

Table A2: Table showing the enriched biological processes of Table A1, ordered by largest % of genes with associated biological process. (1) Enriched processes are shown along with (2) Count of genes associated with said process, (3) % of genes associated with said process from original list (4) P-value of enrichment (5) fold enrichment of functions over the reference gene list, which is all other human genes. Derived from List 1. 

Table A3: Table displaying conversion of protein names from Table A1 to Enterez Gene ID system

Tables_A4_A5_A6.xlsx

Table A4: List of all transcriptional factors extracted from ReMAP, occupying A2UCOE and RPS3 region, ordered by joint ranking, filtered for well-defined transcriptional factors using JASPAR database. Table contains number of sites from combined ChIP experiments separately for both UCOEs and combined. Derived from List 2.

Table A5: Table showing the enriched biological processes of Table A4, ordered by largest % of genes with associated biological process. (1) Enriched processes are shown along with (2) Count of genes associated with said process, (3) % of genes associated with said process from original list (4) P-value of enrichment (5) fold enrichment of functions over the reference gene list, which is all other human genes. Derived from List 2. 

Table A6: Table displaying conversion of protein names from Table A4 to Enterez Gene ID system.

Tables_A7_A8_A9.xslx

Table A7: List of all transcriptional factors extracted from ReMAP, occupying A2UCOE and RPS3 region, ordered by joint ranking, filtered for well-defined transcriptional factors using JASPAR database, filtered for ubiquitous factors using Tsucala, Hussain and Antoniou (unpublished). Table contains number of sites from combined ChIP experiments separately for both UCOEs and combined. Derived from List 3

Table A8: Table showing the enriched biological processes of Table A7, ordered by largest % of genes with associated biological process. (1) Enriched processes are shown along with (2) Count of genes associated with said process, (3) % of genes associated with said process from original list (4) P-value of enrichment (5) fold enrichment of functions over the reference gene list, which is all other human genes. Derived from List 3.

Table A9: Table displaying conversion of protein names from Table A7 to Enterez Gene ID system.

Figures

Figure A1.png

Figure A1: Transcription factor ChIP-seq peaks within the Rps3 UCOE genomic region extracted from the ReMap database. Details of the experiments are on the right of the figure. The dark green bar at the top indicates the Rps3 CpG island (CGI). The black vertical spikes indicate GC content. The dark blue bar indicates the length of the 3.2kb UCOE sequence. The thick and thin blue line indicates the coding and non-coding sections of Rps3. The colours of the bars indicate the target of the ChIP-seq experiment. The small vertical bar in the middle of each peak indicates the point at which the ChIP-seq signal is at its highest.