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euGenes: Homologous Genes Summary Table
Genes with one or more similar genes or homologs in other organisms.Number and percent with homologs, of total protein sequences available per organism.
| Homologs > Source | Fruitfly | Human | Mouse | Mosquito | Weed | Worm | Yeast | Zebrafish | Rat | Rice | E. coli | Chimp | | | Any | N genes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fruitfly | -- | 5959 45% | 5620 42% | 8088 61% | 2617 19% | 4063 31% | 1848 14% | 1082 8% | 0 0% | 2445 18% | 511 3% | 336 2% | | | 8330 63% | 13092 |
| Human | 9451 42% | -- | 17418 78% | 9766 44% | 4444 20% | 7364 33% | 3417 15% | 3741 16% | 0 0% | 4135 18% | 705 3% | 2088 9% | | | 19136 86% | 22058 |
| Mouse | 7158 45% | 14076 89% | -- | 7334 46% | 3445 21% | 5565 35% | 2427 15% | 2642 16% | 0 0% | 3204 20% | 556 3% | 1201 7% | | | 14806 94% | 15706 |
| Mosquito | 9578 61% | 7167 45% | 6680 42% | -- | 3216 20% | 4946 31% | 2257 14% | 1337 8% | 0 0% | 2971 18% | 1024 6% | 420 2% | | | 10415 66% | 15686 |
| Weed | 4763 17% | 5620 21% | 5447 20% | 5128 19% | -- | 3886 14% | 3569 13% | 967 3% | 0 0% | 17894 67% | 1383 5% | 428 1% | | | 18013 67% | 26595 |
| Worm | 4457 24% | 4948 26% | 4642 25% | 4751 25% | 2461 13% | -- | 1800 9% | 961 5% | 0 0% | 2255 12% | 498 2% | 302 1% | | | 5692 30% | 18467 |
| Yeast | 1589 25% | 1766 28% | 1673 26% | 1672 26% | 1757 28% | 1371 22% | -- | 272 4% | 0 0% | 1627 26% | 496 8% | 123 1% | | | 2194 35% | 6200 |
| Zebrafish | 685 53% | 1055 83% | 1032 81% | 667 52% | 206 16% | 487 38% | 137 10% | -- | 0 0% | 194 15% | 53 4% | 160 12% | | | 1064 83% | 1270 |
| Rat | 12244 44% | 25251 90% | 23897 85% | 12655 45% | 5538 19% | 9625 34% | 4377 15% | 5468 19% | -- | 5184 18% | 896 3% | 3267 11% | | | 26986 97% | 27811 |
| Rice | 6719 12% | 5779 11% | 5119 9% | 7553 14% | 25239 48% | 5175 9% | 5160 9% | 845 1% | 0 0% | -- | 1288 2% | 337 0% | | | 25306 48% | 52250 |
| E. coli | 348 8% | 406 9% | 380 9% | 854 20% | 566 13% | 317 7% | 370 8% | 60 1% | 0 0% | 578 13% | -- | 18 0% | | | 1159 27% | 4174 |
| Chimp | 119 14% | 770 95% | 649 80% | 125 15% | 45 5% | 98 12% | 53 6% | 261 32% | 0 0% | 42 5% | 8 0% | -- | | | 771 95% | 810 |
Genes with one or more similar genes, or paralogs, in same organism.
| Fruitfly | Human | Mouse | Mosquito | Weed | Worm | Yeast | Zebrafish | Rat | Rice | E. coli | Chimp | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Paralogs | 4901 37% | 13772 62% | 8502 54% | 7932 50% | 19720 74% | 9996 54% | 2030 32% | 814 64% | 0 0% | 35852 68% | 1194 28% | 668 82% |
Source (rows): source protein for BLAST query
Homologs (columns): sequences in BLAST database match with probability <= 1e-30
Any column: Source organism protein have one or more homologs in any organism
N genes column: Number of protein sequences available for the organism
Methods:
This is a computed gene homology or similarity using reference protein sequences
identified by the source databases. A BLAST of all these sequences is computed,
each sequence against all others, using specific parameters given below.
The sequences used in these calculations are found in the "Reference proteins" data files in each organism's folder. This summary is determined from the "Homologous genes table" data files also in each folder.
The counts in this table are of the number of available genes for an organism, and those which have one or more significant homologs in the other organisms. Percentages are the count of genes with any homolog (one or several) in another organism, divided by the total available genes in that organism (x 100).
You can read the homology summary table best this way. To answer the question what percent of all fruitfly genes have any homologs in C.elegans, look at the Fruitfly row, and find the Worm column. To answer the reverse, the Worm row and Fruitfly column says the percent of all worm genes that have any fruitfly homologs.
Note the asymmetry in these counts and percents. Fruitfly genome may have 5600 of its 13000 genes (43%) showing some homology to Human genes, whereas the Human genome may have 8700 of its 47000 genes (18%) showing some homology to Fruitfly genes. These include the same gene-pairs.
Please note that the summary you find here is based on a specific set of data and homology/similarity (BLAST) calculation parameters. Someone else may publish a different set of values, which would be equally valid, using a different set of data and options for determining "homology". The euGenes summary tries to stay up-to-date by using reference sequences identified by genome databases, and by matching current gene information from these databases with their current sequences.
These values are all moving targets; more data that is coming from genome sequencing projects will change these values. Especially in the euGenes summary, the fruitfly, worm (C.elegans) and yeast data is based on full genome sequences, while man, mouse, weed, and fish are based only on partial sequencing, which may skew values like percent homologies higher than in fact these organisms have.
Homology computations:
blastall -v 10 -b 10 -m 9 -a 4 -p blastp -e 1e-30 -d org1/refprot.fasta -i org2/refprot.fasta
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
Homologous genes for fly computed 31-October-2003 with BLASTP 2.2.6
euGenes uses Argos: A Replicable Genome infOrmation System