An approximate number of human genes, transcripts, proteins and metabolites?

Question

[ahmadbiotech]

Hello Biostars,

What are an approximate quantity of human genes, transcripts (coding transcripts), proteins and metabolites? What about a model plant like Arabidopsis?

Thanks

[IP]

A google search could have pointed you to BioCyC.See the link with E.coli K12 as example

[GenoMax]

While that is true, human part of BioCyc databases requires a paid subscription (most everything besides E. coli does), so it is not generally useful. As @Michael pointed out below this sort of information can be obtained from Ensembl/NCBI etc.

[IP]

Ops, I didn't know that, I just used BioCyc for E.coli, thanks for the infor btw

[Michael]

What have you tried?

[ahmadbiotech]

I just need to know the proportion of genes:transcripts:proteins:metabolites? any answer?

[Michael]

Have you tried anything in the mean time? We value if posters show a reasonable attempt to solve the problem instead of just dumping undigested questions. Hint: where could you find such information?

[ahmadbiotech]

Dear Dondrup, Why do you think the question is undigested? For someone who is working on a transcriptome or proteome, an estimation of transcriptome or ... volume are important. For example for human if we assume there are 20000 protein-coding genes in the genome level (Human genome- Wikipedia), it is interesting that how many transcripts are existed due to different kind of splicing and so on. The proportion of transcripts/genes can help us in some studies, although we know that it is not a static value. So my question is: assuming there are 20000 protein-coding genes in the human genome, These 20000 genes produced how many unique transcripts, How many unique proteins, and how many metabolites? My case study is not Human, but as there are more information on human I asked it about human to just have an estimation.

Best,

[Michael]

Hi Ahmad, I called your question 'undigested' (note: not unjustified, your question is perfectly valid) because you did not show any attempt to solve it yourself nor did you provide any detail on the background of your request. You can find approximate figures for genes, transcripts, and proteins in Ensembl. The only real complicated part is possibly the number of metabolites.

[Pierre Lindenbaum]

this post was cited in https://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=8941&context=etd

Answer 1

[youcai]

Human

• GENCODE

• HGNC

Answer 2

[ahmadbiotech]

Here are some statistics that I found in different databases:

For human:

• Coding genes: about 20,441
• Non-coding genes: about 22,219
• Transcription factors: about 2,067 (TFs/total genes= 10 %)
• Transcripts: about 198,002 (Transcripts/genes = 9.68)
• Proteins: more than 30,057
• Metabolites: more than 42162

Any revision or adding more information to this post would be appreciated,

Answer 3

[Denise CS]

These are some stats for Arabidopsis thaliana regarding genes (protein coding or otherwise) and transcripts. Ensembl Plants BioMart is also a good place to get some statistics (click on the 'count' button once you select your filters). As for metabolites, try Metabolights from EMBL-EBI. It does have data for both human and Arabidopsis. This is the original paper.

[Denise CS]

And this is the Metabolights resource.