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Density of exons per gene

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

genome
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written by 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

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written by jk • jk

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.

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written by WouterDeCoster WouterDeCoster

2 answers

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 |
+-----------------------+
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written by Pierre Lindenbaum Pierre Lindenbaum

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
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written by Renesh Renesh

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