Help
.. Preferences
Help
.. Preferences
| Homologs > Source | Human | Chimp | Dog | Mouse | Rat | Chicken | Pufferfish (Fugu) | Zebrafish | Fruitfly (D.melano.) | Mosquito | Bee | Worm (C.elegans) | Worm (C.briggsae) | Mustard weed | Rice | Soil amoeba (Dicty.) | Yeast (S.cerev.) | Bacteria (E.coli) | | | Any | N genes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Human | -- | 29529 87% | 27761 81% | 26830 79% | 23860 70% | 22947 67% | 22166 65% | 21368 63% | 13276 39% | 13123 38% | 11446 33% | 10538 31% | 10418 30% | 5832 17% | 5210 15% | 5662 16% | 3919 11% | 838 2% | | | 31101 91% | 33860 |
| Chimp | 18898 87% | -- | 16865 78% | 16194 75% | 14283 66% | 13792 64% | 13137 61% | 12579 58% | 7673 35% | 7636 35% | 6532 30% | 6009 27% | 5956 27% | 3430 15% | 3050 14% | 3343 15% | 2358 10% | 499 2% | | | 19179 89% | 21506 |
| Dog | 28144 92% | 27139 89% | -- | 26740 88% | 23816 78% | 23302 76% | 22771 75% | 22053 72% | 13992 46% | 13947 46% | 12092 39% | 11259 37% | 11157 36% | 6249 20% | 5492 18% | 6013 19% | 4177 13% | 952 3% | | | 29034 95% | 30308 |
| Mouse | 16384 86% | 15674 82% | 16066 84% | -- | 14067 74% | 13069 68% | 12662 66% | 12231 64% | 7887 41% | 7789 41% | 6759 35% | 6331 33% | 6268 33% | 3630 19% | 3196 16% | 3558 18% | 2432 12% | 557 2% | | | 17167 90% | 18941 |
| Rat | 12409 94% | 11907 90% | 12184 92% | 12420 94% | -- | 10631 80% | 10412 79% | 10037 76% | 6592 50% | 6521 49% | 5660 43% | 5378 40% | 5298 40% | 3062 23% | 2741 20% | 2974 22% | 2097 15% | 484 3% | | | 12844 97% | 13142 |
| Chicken | 22452 79% | 21676 76% | 22190 78% | 21528 75% | 19697 69% | -- | 20547 72% | 19946 70% | 12368 43% | 12307 43% | 10725 37% | 9997 35% | 9943 34% | 5504 19% | 4866 17% | 5448 19% | 3721 13% | 889 3% | | | 23740 83% | 28416 |
| Pufferfish (Fugu) | 25223 76% | 24411 73% | 24984 75% | 24492 74% | 22639 68% | 23945 72% | -- | 25854 78% | 14835 44% | 14844 44% | 13024 39% | 12108 36% | 11921 36% | 6277 19% | 5603 16% | 6225 18% | 4189 12% | 991 3% | | | 29356 88% | 33003 |
| Zebrafish | 24213 75% | 23096 72% | 23729 74% | 23224 72% | 21507 67% | 22744 70% | 25550 79% | -- | 13041 40% | 13273 41% | 11558 36% | 10588 33% | 10329 32% | 5547 17% | 5109 15% | 5572 17% | 3695 11% | 860 2% | | | 28224 88% | 32062 |
| Fruitfly (D.melano.) | 6057 44% | 5636 41% | 5997 44% | 5900 43% | 5387 39% | 5539 41% | 5882 43% | 5421 40% | -- | 8161 60% | 5980 44% | 4632 34% | 4581 34% | 2742 20% | 2421 17% | 2708 20% | 1925 14% | 485 3% | | | 11259 83% | 13472 |
| Mosquito | 6856 43% | 6327 40% | 6759 42% | 6662 42% | 6099 38% | 6288 39% | 6680 42% | 6212 39% | 9437 59% | -- | 6854 43% | 5198 32% | 5107 32% | 3089 19% | 2735 17% | 2994 18% | 2169 13% | 778 4% | | | 10282 65% | 15802 |
| Bee | 8795 51% | 8281 48% | 8627 50% | 8517 50% | 7810 46% | 8186 48% | 8657 51% | 8166 48% | 10209 60% | 10206 60% | -- | 6525 38% | 6411 37% | 3292 19% | 2957 17% | 3286 19% | 2315 13% | 551 3% | | | 11563 68% | 16948 |
| Worm (C.elegans) | 5019 25% | 4568 23% | 4922 24% | 4891 24% | 4490 22% | 4612 23% | 4824 24% | 4519 22% | 4685 23% | 4709 23% | 3817 19% | -- | 14883 75% | 2567 12% | 2297 11% | 2495 12% | 1829 9% | 480 2% | | | 15003 75% | 19764 |
| Worm (C.briggsae) | 4949 25% | 4504 23% | 4860 24% | 4811 24% | 4419 22% | 4588 23% | 4771 24% | 4424 22% | 4615 23% | 4597 23% | 3757 19% | 14329 73% | -- | 2494 12% | 2226 11% | 2430 12% | 1800 9% | 469 2% | | | 14383 73% | 19528 |
| Mustard weed | 5527 19% | 5040 17% | 5410 18% | 5460 18% | 4881 16% | 5024 17% | 5404 18% | 4904 16% | 4753 16% | 4831 16% | 3812 13% | 4491 15% | 4399 15% | -- | 17730 61% | 5086 17% | 3612 12% | 1326 4% | | | 18356 63% | 28860 |
| Rice | 4649 9% | 4208 8% | 4532 9% | 4584 9% | 4151 8% | 4174 8% | 4634 9% | 4438 9% | 3937 8% | 4079 8% | 3148 6% | 3708 7% | 3637 7% | 16808 34% | -- | 4180 8% | 3051 6% | 1254 2% | | | 17453 36% | 48467 |
| Soil amoeba (Dicty.) | 3044 22% | 2722 19% | 2996 21% | 2948 21% | 2622 19% | 2745 20% | 2924 21% | 2745 20% | 2614 19% | 2609 19% | 2119 15% | 2408 17% | 2362 17% | 2758 20% | 2475 18% | -- | 1900 13% | 524 3% | | | 3939 28% | 13671 |
| Yeast (S.cerev.) | 1785 30% | 1617 27% | 1763 30% | 1733 29% | 1614 27% | 1593 27% | 1710 29% | 1579 27% | 1675 28% | 1665 28% | 1280 22% | 1541 26% | 1514 26% | 1732 29% | 1559 26% | 1650 28% | -- | 473 8% | | | 2833 49% | 5777 |
| Bacteria (E.coli) | 412 9% | 355 8% | 394 9% | 388 9% | 349 8% | 372 8% | 390 9% | 348 8% | 365 8% | 668 15% | 278 6% | 350 8% | 351 8% | 574 13% | 543 12% | 431 10% | 369 8% | -- | | | 1062 25% | 4242 |
| Human | Chimp | Dog | Mouse | Rat | Chicken | Pufferfish (Fugu) | Zebrafish | Fruitfly (D.melano.) | Mosquito | Bee | Worm (C.elegans) | Worm (C.briggsae) | Mustard weed | Rice | Soil amoeba (Dicty.) | Yeast (S.cerev.) | Bacteria (E.coli) | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Paralogs | 23366 69% | 9941 46% | 21728 71% | 10735 56% | 7205 54% | 18226 64% | 22907 69% | 24431 76% | 4993 37% | 7037 44% | 8411 49% | 9240 46% | 8988 46% | 21461 74% | 25802 53% | 5276 38% | 1930 33% | 1155 27% |
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:
BLAST: BLASTP 2.2.10 [Oct-19-2004]
CMDLINE: blastall -v 10 -b 10 -m 9 -p blastp -e 1e-3
DATE: August-2005
Database: Database: /gpfs/ux455375/prots/protdb/sanPF
minbits: 0
mineval: 1e-30
minident: 0