Density of exons per gene

Question

[jk]

Hi All,

It would be great if anyone can let me know. How can the density of exons per gene to be calculated?

At last need a single density value per gene

Regards, JK

[jk]

Hi Renesh and Pierre,

Thanks for the prompt replies.

I was actually looking for something per gene, like:

gene1 <- density_per_exon

gene2 <- density_per_exon

etc..

How do we consider varying exon length and varying gene length into consideration. eg:

refseq_id chrom strand tx_start tx_end cdsStart cdsEnd exonCount exonStarts exonEnds

NM_008302 chr2 - 45704726 45710210 45704963 45708860 11 "45704726,45705177,45705806,45706188,45706418,45707206,45707614,45707966,45708361,45708713,45710115," "45705073,45705511,45706075,45706336,45706775,45707515,45707748,45708126,45708568,45708860,45710210,"

NM_010106 chr2 - 78326260 78329531 78326540 78328461 8 "78326260,78326764,78327084,78327430,78327658,78328047,78328317,78329445," "78326665,78326999,78327341,78327581,78327955,78328227,78328495,78329531,"

NM_008302 have 11 exons with gene length 5484 (45710210 - 45704726)

NM_010106 have 8 exons with gene length 3271 (78329531 - 78326260)

Regards, JK

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Answer 1

[Pierre Lindenbaum]

using ucsc/mysql

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg38 -e 'select   (select count(distinct E.chrom,E.chromStart,E.chromEnd) from wgEncodeGencodeAttrsV27 as A ,wgEncodeGencodeExonSupportV27 as E where E.transcriptId=A.transcriptId) / (select count(distinct geneId) from wgEncodeGencodeAttrsV27 as A ,wgEncodeGencodeExonSupportV27 as E where E.transcriptId=A.transcriptId) as density_exon_per_gene'
+-----------------------+
| density_exon_per_gene |
+-----------------------+
|                9.5074 |
+-----------------------+

Answer 2

[Renesh]

You can calculate the density of the exons per gene as below,

1. Download the gff/gtf file for given organism from respective database (Eg. Ensemble, Phytozme etc.)
2. Calculate the total number of exons for all genes
3. Get a count of a total number of genes for that organism. You can also calculate this from gtf/gff file
4. Exons density = total number of exons/ total number of genes