|
Category
|
Number of entries
|
Source
|
Example fields from this category
|
| Genes |
42,716 |
UCSC Genome Browser's track UCSC Known Genes. Click here for restrictions on use |
orientation, exons, CDS |
| Genes with product and function data |
36,412 |
Locus Link |
product, biological process, cellular component, molecular function |
| Expression data |
2,297,169 |
UniGene at NCBI |
tissue, gene ID |
| Microarray expression data |
38,563 |
GNF |
tissue, expression level |
| Genetic Disorders |
6,485 |
OMIM |
disorder, gene ID |
| Gene Orthologs |
0 |
Database of evolutionary distances and Ensembl |
species, gene symbol, coordinates in other species, percent CDS identity,percent protein identity |
| RNA Genes |
7,113 |
UCSC Genome Browser |
name, score, source, type, is pseudo, ... |
| Alternate Gene Model: Ensembl Genes |
29,798 |
UCSC Genome Browser |
orientation, exons, CDS |
| Alternate Gene Model: Geneid Genes |
31,803 |
UCSC Genome Browser |
orientation, exons, CDS |
| Alternate Gene Model: Genscan Genes |
42,376 |
UCSC Genome Browser |
orientation, exons, CDS |
| Alternate Gene Model: MGC Genes |
16,110 |
UCSC Genome Browser |
orientation, exons, CDS |
| Alternate Gene Model: RefSeq Genes |
19,752 |
UCSC Genome Browser |
orientation, exons, CDS |
| Alternate Gene Model: SGP Genes |
42,677 |
UCSC Genome Browser |
orientation, exons, CDS |
| Alternate Gene Model: Twinscan Genes |
25,166 |
UCSC Genome Browser |
orientation, exons, CDS |
| Human ESTs |
4,917,664 (24,470,824 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| Human mRNAs |
144,855 (1,026,264 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| NonHuman ESTs |
17,673,833 (49,246,320 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| NonHuman mRNAs |
526,512 (2,642,847 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| Spliced ESTs |
2,296,567 (16,824,547 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| TIGR Gene Index |
280,734 (1,218,611 exons) |
UCSC Genome Browser |
name, score, strand, exon coordinates |
| UniGene |
114,115 (548,995 exons) |
UCSC Genome Browser |
name, score, strand, exon coordinates |
| Multiple alignments |
8,561,326 |
UCSC Genome Browser and Penn State - Bioinformatics Group scoring using humor |
score |
| Local alignments human vs. chicken |
407,847 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. chicken |
3,006,490 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments human vs. fugu |
327,413 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. fugu |
1,410,400 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments human vs. mouse |
1,717,960 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. mouse |
36,360,012 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments human vs. rat |
2,716,503 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. rat |
32,784,849 |
UCSC Genome Browser and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| 3-way conserved |
3,503,611 |
Penn State - Bioinformatics Group |
repetitive element |
| Fugu blat alignments |
726,051 alignment blocks |
UCSC Genome Browser |
matches, mismatches, ... |
| mouse net alignments |
10,191,660 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| rat net alignments |
10,204,329 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| chicken net alignments |
885,797 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| Regulatory potential score (based on hmr alignments) |
167,348,348 |
Penn State - Bioinformatics Group |
score |
| Conservation score based on 5-way alignments |
517,674,326 |
UCSC Genome Browser |
score |
| Transcription factor binding sites |
211,974,247 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score for 166 matrices |
| Conserved Transcription factor binding sites (hmr) |
4,993,567 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score for 165 matrices |
| ChIP-chip data from affymetrix |
1,154 |
Human Transcriptome Project |
factor |
| Known regulatory regions |
93 |
Penn State - Bioinformatics Group |
name |
| Functional promoters |
153 |
Stanford |
|
| Predicted promoters |
40,405 |
Stanford
Downloaded from UCSC Genome Browser |
|
| Micro RNA |
176 |
Vertebrate microRNA genes |
name |
| CpG islands |
257,361 |
UCSC Genome Browser |
name |
| SNPs |
4,948,761 |
dbSNP
and UCSC Genome Browser |
type, allele, frequency |
| HbVar: A Database of Human Hemoglobin Variants and Thalassemias |
1,115 variants |
HbVar |
type, HbVar ID |
| Repeats |
4,975,669 |
UCSC Genome Browser |
name, class, family |
| Recombination rates |
8,454 |
deCODE Genetics
Marshfield
Genethon
Downloaded from UCSC Genome Browser |
recombination rate; sex averaged, F, and M |
| GC percent |
153,518 |
UCSC Genome Browser |
percent |
| Isochore |
10,251 |
Anton Nekrutenko's Group |
percent |
| Restriction sites |
116,981,108 |
Penn State - Bioinformatics Group |
for 128 different enzymes |