|
Category
|
Number of entries
|
Source
|
Example fields from this category
|
| Genes |
42,944 |
Locus Link and Refseq gene track at UCSC |
orientation, exons, CDS |
| Genes with product and function data |
36,843 |
Locus Link |
product, biological process, cellular component, molecular function |
| Expression data |
749,891 |
UniGene at NCBI |
tissue, gene ID |
| Microarray expression data |
36,251 |
GNF |
tissue, expression level |
| Genetic Disorders |
6,824 |
OMIM |
disorder, gene ID |
| Gene Orthologs |
53,692 |
Database of evolutionary distances and Ensembl |
species, gene symbol, coordinates in other species, percent CDS identity,percent protein identity |
| Alternate Gene Model: Geneid Genes |
31,935 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Genscan Genes |
42,400 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: MGC Genes |
17,871 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: RefSeq Genes |
21,730 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: SGP Genes |
33,333 |
UCSC Golden Path |
orientation, exons, CDS |
| Alternate Gene Model: Twinscan Genes |
25,633 |
UCSC Golden Path |
orientation, exons, CDS |
| Human ESTs |
5,623,452 (26,496,760 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| Human mRNAs |
153,347 (1,073,448 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| NonHuman ESTs |
20,100,409 (55,625,768 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| NonHuman mRNAs |
576,832 (2,865,834 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| Spliced ESTs |
2,438,844 (17,622,811 exons) |
UCSC Genome Browser |
matches, mismatches, ... |
| Multiple alignments |
50,937,020 |
UCSC Golden Path and Penn State - Bioinformatics Group scoring using multiz |
score |
| Local alignments human vs. chicken |
321,066 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. chicken |
2,710,555 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments human vs. mouse |
1,857,501 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. mouse |
33,865,229 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Local alignments human vs. rat |
1,789,804 |
UCSC Golden Path and Penn State - Bioinformatics Group |
score, lav file sequence and header fields |
| Gap free alignments human vs. rat |
32,976,304 |
UCSC Golden Path and Penn State - Bioinformatics Group |
percent identity, local alignment ID |
| Fugu blat alignments |
214,990 |
UCSC Golden Path |
matches, mismatches, ... |
| dog net alignments |
9,221,722 |
UCSC Genome Browser | score, level, gaps, repeat bases, N bases, ... |
| mouse net alignments |
10,373,335 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| rat net alignments |
10,219,335 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| chicken net alignments |
951,653 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| chimp net alignments |
1,274,363 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| zebrafish net alignments |
883,289 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| fugu net alignments |
549,883 |
UCSC Genome Browser |
score, level, gaps, repeat bases, N bases, ... |
| Regulatory potential score (based on hmr alignments) |
162,260,706 |
Penn State - Bioinformatics Group |
score |
| Transcription factor binding sites |
242,918,236 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score |
| Conserved Transcription factor binding sites (hg17Mm5Rn3Canfam1) |
2,963,975 |
Penn State - Bioinformatics Group and
TRANSFAC (free registration required) |
factor, strand, score |
| ChIP-chip data from affymetrix |
1,154 |
Human Transcriptome Project |
|
| Known regulatory regions |
93 |
Penn State - Bioinformatics Group |
name |
| Fun
ctional promoters |
150 |
Stanford |
|
| Predicted promoters |
40,360 |
Stanford
Downloaded from UCSC Golden Path |
|
| Micro RNA |
221 |
UCSC Golden Path |
name |
| CpG islands |
27,437 |
UCSC Golden Path |
name |
| SNPs |
0 |
dbSNP
and UCSC Golden Path |
type, allele, frequency |
| HbVar: A Database of Human Hemoglobin Variants and Thalassemias |
1,425 variants |
HbVar |
type, HbVar ID |
| Repeats |
4,993,515 |
UCSC Golden Path |
name, class, family |
| Recombination rates |
8,454 |
deCODE Genetics
Marshfield
Genethon
Downloaded from UCSC Golden Path |
recombination rate; sex averaged, F, and M |
| GC percent |
153,850 |
Penn State - Bioinformatics Group |
percent |
| Isochore |
10,211 |
Anton Nekrutenko's Group |
percent |
| Restriction sites |
117,364,635 |
Penn State - Bioinformatics Group |
for 0 different enzymes |