Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Repositories
  • ArrayExpress (133)
  • BioProject (153)
  • ClinVar (2)
  • Dryad (16)
  • Figshare (6)
  • GEMMA (9)
  • OmicsDI (104)
  • PDB (20)
  • PDBe:EMDB (1)
  • UniProt:Swiss-Prot (5)
  • YPED (1)
  • dbGaP (1)

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.

Displaying 16 of 16 results for "TFAM"
i
Switch View:
Sorted By:
Title Date Issued Date Released Description
Devil TFAM file
06-29-2015 06-29-2015
TFAM file with individual devil details for PLINK
UCD_2014.tfam
03-30-2015 03-30-2015
PLINK GWAS file
Imputed Data (.tfam)
11-25-2015 11-25-2015
n/a
goat_data2_dryad
07-27-2016 07-27-2016
the corresponding tfam file
resequencing_collaredFlycatcherGenotypes
12-10-2015 01-06-2016
This is the PLINK .tfam format file for the genotypes of the 81 genome-resequenced male collared flycatchers.
snpChipGWASTfamFile_27Nov2015
12-10-2015 01-06-2016
This is the .tfam file for the SNP chip data set.
snpChipGWASTpedFile_27Nov2015
12-10-2015 01-06-2016
This file contains the SNP chip genotypes in PLINK .tped format. The genotypes are linked to identifications by the associated .tfam file.
nacanids_111indiv_unrel_noYNP_42Ksnps.tfam
09-02-2015 09-03-2015
The .tfam file, in PLINK format, that corresponds to nacanids_111indiv_unrel_noYNP_42Ksnps.tped. This file has the sample names for 111 unrelated wolves.
Data from: Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and non-parallel physiological divergence
07-25-2012 09-07-2012
Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved “dwarf” and “normal” sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with all five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation, and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further examination of the links between this critical physiological pathway and ecological and genetic variation will provide insight into the fine-scale evolutionary dynamics at work in nature.
nacanids_123indiv_unrel_42Ksnps_CoatColor_wYNP_n33_black.tfam
09-02-2015 09-03-2015
PLINK formatted TFAM file with coat color genotype for each of 33 wolves. Individuals coded as a 2 are black, individuals coded as a 1 are not black (can be white or gray).
nonAdmix_nacanids_94indiv_unrel_noYNP_42Ksnps_wEcotypes.tfam
09-02-2015 09-03-2015
The corresponding TFAM file for the set of 94 unrelated individuals showing >50% assignment in structure. The first column of each line is the ecotype designation for each sample.
nacanids_unrel_42Ksnps_CoatColor_wYNP_n33_white.tfam
09-02-2015 09-03-2015
PLINK formatted TFAM file with coat color genotype for each of 33 wolves. Individuals coded as a 2 are white, individuals coded as a 1 are not white (can be black or gray).
Data from: P53 gene discriminates two ecologically divergent sister species of pine voles
04-06-2015 03-09-2016
Genes with relevant roles in the differentiation of closely-related species are likely to have diverged simultaneously with the species and more accurately reproduce the species tree. The Lusitanian (Microtus lusitanicus) and Mediterranean (M. duodecimcostatus) pine voles are two recently separated sister species with fossorial lifestyles whose different ecological, physiological and morphological phenotypes reflect the better adaptation of M. duodecimcostatus to the underground habitat. Here we asked whether the differentiation of M. lusitanicus and M. duodecimcostatus involved genetic variations within the tumour suppressor p53 gene, given its role in stress-associated responses. We performed a population-genetic analysis through sequencing of exons and introns of p53 in individuals from sympatric and allopatric populations of both the species in the Iberian Peninsula in which a unidirectional introgression of mitochondrial DNA was previously observed. We were able to discriminate the two species to a large extent. We show that M. duodecimcostatus is composed of one genetically unstructured group of populations sharing a P53 protein that carries a mutation in the DNA-binding region not observed in M. lusitanicus, raising the possibility that this mutation may have been central in the evolutionary history of M. duodecimcostatus. Our results provide suggestive evidence for the involvement of a master transcription factor in the separation of M. lusitanicus and M. duodecimcostatus during Microtus radiation in the Quaternary presumably via a differential adaptive role of the novel p53 in M. duodecimcostatus.
Data from: Evidence for amino acid snorkeling from a high-resolution, in vivo analysis of Fis1 tail anchor insertion at the mitochondrial outer membrane
12-22-2016 03-09-2017
Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiae Fis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of the Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl-terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening of the Fis1p TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs to distinct organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong, in vivo evidence that lysine and arginine can "snorkel," or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.
Data from: Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri
10-16-2013 12-13-2013
Marine organisms are commonly exposed to variable environmental conditions and many of them are under threat from increased sea temperatures caused by global climate change. Generating transcriptomic resources under different stress conditions are crucial for understanding molecular mechanisms underlying thermal adaptation. In this study, we conducted transcriptome-wide gene expression profiling of the scallop Chlamys farreri challenged by acute and chronic heat stress. Of the 13,953 unique tags, more than 850 were significantly differentially expressed at each time point after acute heat stress, which was more than the number of tags differentially expressed (320~350) under chronic heat stress. To obtain a systemic view of gene expression alterations during thermal stress, a weighted gene coexpression network was constructed. Six modules were identified as acute heat stress-responsive modules. Among them, four modules involved in apoptosis regulation, mRNA binding, mitochondrial envelope formation, and oxidation reduction were down-regulated. The remaining two modules were up-regulated. One was enriched with chaperone, and the other with microsatellite sequences, whose coexpression may originate from a transcription factor binding site. These results indicated that C. farreri triggered several cellular processes to acclimate to elevated temperature. No modules responded to chronic heat stress, suggesting that the scallops might have acclimated to elevated temperature within 3 days. This study represents the first sequencing-based gene network analysis in a non-model aquatic species and provides valuable gene resources for the study of thermal adaptation, which should assist in the development of heat-tolerant scallop lines for aquaculture.
Data from: The role of ontogeny in physiological tolerance: decreasing hydrostatic pressure tolerance with development in the northern stone crab Lithodes maja
06-03-2015 06-03-2015
Extant deep-sea invertebrate fauna represent both ancient and recent invasions from shallow-water habitats. Hydrostatic pressure may present a significant physiological challenge to organisms seeking to colonize deeper waters or migrate ontogenetically. Pressure may be a key factor contributing to bottlenecks in the radiation of taxa and potentially drive speciation. Here, we assess shifts in the tolerance of hydrostatic pressure through early ontogeny of the northern stone crab Lithodes maja, which occupies a depth range of 4–790 m in the North Atlantic. The zoea I, megalopa and crab I stages were exposed to hydrostatic pressures up to 30.0 MPa (equivalent of 3000 m depth), and the relative fold change of genes putatively coding for the N-methyl-d-aspartate receptor-regulated protein 1 (narg gene), two heat-shock protein 70 kDa (HSP70) isoforms and mitochondrial Citrate Synthase (CS gene) were measured. This study finds a significant increase in the relative expression of the CS and hsp70a genes with increased hydrostatic pressure in the zoea I stage, and an increase in the relative expression of all genes with increased hydrostatic pressure in the megalopa and crab I stages. Transcriptional responses are corroborated by patterns in respiratory rates in response to hydrostatic pressure in all stages. These results suggest a decrease in the acute high-pressure tolerance limit as ontogeny advances, as reflected by a shift in the hydrostatic pressure at which significant differences are observed.