bioinfo.na.iacr.it/ALE-HSA21

1. ALE-HSA21 is accessible at: http://bioinfo.na.iac.cnr.it/ALE-HSA21 The following pages are a schematic representation of how to navigate through ALE-HSA21 website and to extract information of interest. • The “core” of ALE-HSA21 website is made of two main sections: • Coding Genes • Non Coding Genes

2. By clicking here the user can access the “General Table” of all the genes annotated on the human chromosome 21 (HSA21). By clicking here the user can access the “General Table” containing 7 HSA21 genes with 12 novel transcripts identified by our group. For sake of simplicity, for the “Coding Genes” section of ALE-HSA21, only examples about “Annotated Genes” are shown in the next pages. The “Novel Genes” subsection contains the same type of information, and has been developed with the same rationale.

3. 1 2 1 2 This is the “General Table” for “Annotated Genes” in which all currently annotated transcripts of HSA21 genes are listed. This Table summarizes primary info such as gene symbols (in alphabetical order), transcript ID, genomic coordinates, sense of transcription (strand), number of exons and (if any) UniProt ID. The “Gene symbol” ( ), the “ID” ( ), the “Genomic coordinates” and the “UniProt ID” are clickable elements. As shown in the black box, by clicking the “Genomic coordinates” the user is directly linked to an “ad hoc created” Session of UCSC Genome Browser containing RNA-Seq coverage data, ENCODE ChIP-Seq data for transcription factors and Ensembl, RefSeq and UCSC genomic annotations

4. “HOW TO EXTRACT INFORMATION FOR CODING GENES IN ALE-HSA21” By clicking the “ID” of interest the user access the “Transcript-specific” page By clicking the “GENE SYMBOL” of interest the user access the “Gene-specific” page “Gene-specific” page “Transcript-specific” page 2 1 Both “Gene-specific” and “Transcript-specific” pages contain 3D exon/intron structures. Each element (promoter, exon, intron and 3’ UTR ) is independently clickable, allowing to access the results of the computational predictive analysis of regulatory sequences, performed as described in the Method Section.

5. “Gene-specific” page On the right panel are schematically described the different areas of this web page Official gene symbol Gene name Gene description Links to external databases Image legend 3 3 6 4 5 6 4 5 1 Interactive 3D transcript models. Each element ( , , , ) is independently clickable)

6. “Transcript-specific” page This web page is dedicated to a specific transcript of interest. Here the user can access different type of data, simply by clicking each element of the transcript (promoter, exon, intron or 3’ UTR). In the following pages are described in detail, step-by-step, all the information the user can retrieve by clicking on: Note to the user: 1 4 4 6 5 3 6 5 3 2 Promoter (defined as ±1kb from the TSS, transcription start site); All information about promoter, exon, intron or 3’ UTR can be accessed both from this “transcript-dedicated” web page and from the “gene-dedicated” web page (previously described in ), simply by clicking on the elements of interest within the 3D model. Exons; Introns; 3’ UTR (untranslated regions);

7. Predictive analysis of Transcription Factors’ (TFs) binding sites within promoters Direct access to the sequence of the promoter in FASTA format. Direct link to a Session of Genome Browser ad hoc created for ALE-HSA21 containing ENCODE ChIP-Seq data for transcription factors falling within the promoter of interest Human TFs predicted to bind the specific sequence Orientation of TF’s binding on DNA Predicted TF’s binding site within the sequence 3d 3e 3f 3b 3c 3c 3d 3b 3f 3e 3a 3a 3 Position of the predicted TF’s binding site within the sequence of interest Weight score provided by RSAT (http://rsat.ulb.ac.be) Download FASTA sequence of the promoter (±1kb from the transcription start site)

8. Predictive analysis of splicing regulatory sequences within exons/introns Direct link to the sequence of interest in FASTA format Binding motif recognized by the splicing factor and and Category of the regulatory sequence (Exonic or intronic splicing enhancher/silencer, ESE/ESS and ISE/ISS) Splicing factor and and Sequence recognized by the splicing factor and surrounding nucleotides within the analyzed element and Position of the binding motif within the sequence of interest 4d 4e 4f 5f 5e 5d 5b 4b 4c 5c 5b 4e 5e 5d 4d 4f 4b 4c 5c 5f 5a 5a 4a 4a Download the sequence in FASTA format 4 5

9. Predictive analysis of miRNA binding sites within 3’ UTRs Direct link to the sequence of interest in FASTA format. Download FASTA sequence of 3’ UTR 6f 6e 6d 6b 6c 6f 6e 6d 6c 6b 6a 6a 6 Human miRNA predicted to bind the analyzed sequence miRNA seed Position of the predicted miRNA binding site (miRNA responsive element, MRE) within the sequence of interest Match between miRNA and the sequence of interest. Exact match to positions 2-8 of the mature miRNA (seed + position 8) followed by an 'A’ is indicated as “8mer-1a”; “7mer-m8” indicates an exact match to positions 2-8 of the mature miRNA (the seed + position 8); “7mer-1a” indicates an exact match to positions 2-7 of the mature miRNA (the seed) followed by an 'A’ (from TargetScan, http://www.targetscan.org) miRNA ID from miRBase database (http://www.mirbase.org)

10. Similarly to the “Coding Genes”, this is the “General Table” in which all the transcripts of HSA21 genes currently annotated as “non-protein coding” are listed. The first column indicates the non-coding category. “Gene symbol”, “ID” and “Genomic coordinates” are clickable elements.

11. “HOW TO EXTRACT INFORMATION FOR NON CODING GENES IN ALE-HSA21” By clicking the “ID” of interest the user access the “Transcript-specific” page By clicking the “GENE SYMBOL” of interest the user access the “Gene-specific” page “Transcript-specific” page “Gene-specific” page C A B Results of the computational predictions are available for the following categories: lincRNAs and pseudogenes  miRNA binding sites predictions within the entire transcript miRNAs and snoRNAs  secondary structure predictions miRNAs  target genes predictions

12. Predictive analysis of miRNA binding sites within lincRNAs and pseudogenes Clickable element to access the predictive analysis of MREs Download FASTA sequence of the entire transcript A5 A3 A4 A1 A2 A5 A4 A2 A1 A3 A Human miRNA predicted to bind the analyzed sequence miRNA seed Position of the predicted miRNA binding site (miRNA responsive element, MRE) within the sequence of interest Match between miRNA and the sequence of interest. Exact match to positions 2-8 of the mature miRNA (seed + position 8) followed by an 'A’ is indicated as “8mer-1a”; “7mer-m8” indicates an exact match to positions 2-8 of the mature miRNA (the seed + position 8); “7mer-1a” indicates an exact match to positions 2-7 of the mature miRNA (the seed) followed by an 'A' miRNA ID from miRBase database (http://www.mirbase.org)

13. Prediction of secondary structure for snoRNAs and miRNAs B1 B2 B1 B1 B2 B Download FASTA Secondary structure predictions Mature miRNA sequence Download FASTA

14. Predictive analysis of miRNAs’ target genes Clickable element to access the predictive target genes C3 C4 C1 C2 C2 C4 C1 C3 C Download FASTA Validated target genes of a specific miRNA according to miRWalk database (http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/genetarget.html ) Predicted target genes of a specific miRNA according to miRWalk database (http://www.umm.uni-heidelberg.de/apps/zmf/mirwalk/predictedmirnagene.html ) Predicted target genes of a specific miRNA according to co-expression data of CoMeTa database (http://cometa.tigem.it) Venn diagrams showing the intersection of the three target genes’ lists