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1 as provided by the Allen Brain Connectivity Atlas.
2 blish a desiccation-tolerance transcriptomic atlas.
3 and analysis using a probabilistic brainstem atlas.
4 om independent patients in The Cancer Genome Atlas.
5 ll tumor types studied via The Cancer Genome Atlas.
6 eplicated in NTL data from The Cancer Genome Atlas.
7 sion locations were mapped to a common brain atlas.
8 5 International Diabetes Federation Diabetes Atlas.
9 , 2015) were obtained from The Cancer Genome Atlas.
10 n a scale-invariant, interactive mouse brain atlas.
11 3 cancer types profiled by The Cancer Genome Atlas.
12 in other cancer types from The Cancer Genome Atlas.
13 d in a validation set from The Cancer Genome Atlas.
14 mor subtypes obtained from The Cancer Genome Atlas.
15 ive scale by projects such as the Human Cell Atlas.
16 inoma patient cohorts from The Cancer Genome Atlas.
17 n independent samples from The Cancer Genome Atlas.
18 molecular data types from The Cancer Genome Atlas.
19 er using patient data from The Cancer Genome Atlas.
20 munofluorescence data from the Human Protein Atlas.
21 omically discriminated using a probabilistic atlas.
22 e, and lesions were mapped to a common brain atlas.
23 se structures using an existing histological atlas.
24 ons in mutants, and to map them onto a brain atlas.
25 enomic datasets, including The Cancer Genome Atlas.
26 scriptome by using data from the Allen Brain Atlas.
27 or data sets obtained from The Cancer Genome Atlas.
28 nning 19 cancer types from The Cancer Genome Atlas.
29 g on almost 200 cases from The Cancer Genome Atlas.
30 gative (TNBC) cancers from The Cancer Genome Atlas.
31 atic mutations reported in The Cancer Genome Atlas.
32 ty in patient tumours from The Cancer Genome Atlas.
33 tory analyses of all networks from the Power atlas.
34 ic data from Allen Human Brain and BrainSpan atlases.
35 markedly from common gyral-based structural atlases.
36 ving the way for systematic charting of cell atlases.
37 n a validation cohort from The Cancer Genome Atlas (113 patients with colorectal tumors, 178 endometr
40 ene expression analysis of The Cancer Genome Atlas AML data set reveals that GLI3 expression is silen
44 inct cancer data sets from The Cancer Genome Atlas and discuss how predictions from these algorithms
46 f ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE to demonstrate its wide applicabil
47 m miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RN
48 e atlas with data from the Allen Human Brain atlas and identified receptor- and transporter-specific
56 351 localized ccRCCs from The Cancer Genome Atlas and validated lncRNA-based recurrence classificati
57 isons by co-registering functional reference atlases and in vivo two-photon fluorescence microscopy d
59 mbine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian
60 en Institute for Brain Science transcriptome atlas, and regional white matter connectivity loss at th
62 es were extracted from the Allen Human Brain Atlas, and their average profile across the cortex was c
65 fied using a standardized region-of-interest atlas applied to the spatially normalized gray matter im
67 for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects a
68 To assess the patient-dependent accuracy of atlas-based attenuation correction (ATAC) for brain posi
74 n to the voxel-intensity histogram within an atlas-based white matter region and using the center and
75 d: whole cerebellum, cerebellar gray matter, atlas-based white matter, and subject-specific white mat
76 when patient bone was used for AC instead of atlas bone, the overall difference of PET with ATACpatie
78 ortantly, interrogation of the Cancer Genome Atlas breast invasive carcinoma data set indicates that
79 f subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody
82 e present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at
83 tient-specific anatomic differences from the atlas causes bone attenuation differences and misclassif
84 renal cancer subtypes from The Cancer Genome Atlas: clear cell renal cell carcinoma (ccRCC, also know
86 colorectal carcinomas from the Cancer Genome Atlas collection to determine whether expression of PPP1
89 ions, we built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862
92 C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmenta
93 we report the generation of a transcriptome atlas covering most phases in the life cycle of the mode
94 Here we first analyzed The Cancer Genome Atlas data and determined that the PTPRT promoter is fre
95 tudies and the analyses of The Cancer Genome Atlas data demonstrate improved results compared with ex
96 its clinical utility with The Cancer Genome Atlas data demonstrated that our algorithm offers more c
99 ternational Consortium and The Cancer Genome Atlas data, copy number and expression agreement in Canc
101 Mining breast cancer TCGA (The Cancer Genome Atlas) data sets, we demonstrate that hnRNPF negatively
102 ors (TFs), our analysis of The Cancer Genome Atlas database (TCGA) found that patients with lower exp
104 Further, an analysis of The Cancer Genome Atlas database indicated that this personalized medicine
106 of human breast tumors in The Cancer Genome Atlas database showed that although RASA1 mutations are
110 computational methods and The Cancer Genome Atlas dataset analysis to identify novel miRNAs that tar
113 Power spectra of 1-s long data segments for atlas-defined brain areas were clustered into spectral p
114 scaled below 42 HU for ZTACSEC For ATAC, the atlas deformed to MR in-phase was segmented to air, inne
116 rred at a 3% to 4% rate in The Cancer Genome Atlas-derived and in-house cohorts of patients with sero
117 e 1000 Genomes Project and The Cancer Genome Atlas, establishing damage as a pervasive cause of seque
120 usly uncharacterized and important molecular atlas for exploring region-specific astroglial functions
122 cs tools: (i) an integrative gene expression atlas for four model legumes that include 550 array hybr
124 as and additional individual fetal brain MRI atlases for completely automatic multi-atlas segmentatio
128 hat NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven compa
129 ly, it has been recently proposed to perform atlas-free random brain parcellation into nodes and alig
130 new algorithm to construct a spatiotemporal atlas from MRI of 81 normal fetuses scanned between 19 a
131 lysis of RNA-seq data from The Cancer Genome Atlas further demonstrated that concordant upregulation
132 -induced gene signature to The Cancer Genome Atlas glioblastoma dataset to explore the association of
134 Our comprehensive human and mouse islet GPCR atlas has demonstrated that species differences do exist
136 nctional architecture, yet current reference atlases have major limitations such as lack of whole-bra
141 alteration frequencies to The Cancer Genome Atlas identified some differences and suggested an enric
142 specification and differentiation genes, our atlas identifies and molecularly characterizes 605 bilat
143 gnature genes derived from the Human Protein Atlas in the EoE transcriptome and in EPC2 esophageal ep
145 al subdivisions, presented in the form of an atlas including confocal sections and 3D digital models
147 on normal-tumor pairs from The Cancer Genome Atlas indicated that cancer-specific expression-associat
148 ransformation of the PET-derived human brain atlas into a protein density map of the serotonin (5-hyd
149 cancer types/subtypes from The Cancer Genome Atlas into over 170,000 carefully curated nonredundant p
156 ent cohorts: a cohort from The Cancer Genome Atlas (n = 532), a cohort from University of Texas South
157 oma subtypes with those of The Cancer Genome Atlas Network and found consistency between the two stud
158 characterization of CRC by The Cancer Genome Atlas Network detected the overexpression of the insulin
161 e database, EnhancerAtlas, which contains an atlas of 2,534,123 enhancers for 105 cell/tissue types.
162 ript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence
168 r Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving 22,000 gene
170 a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT1
171 Our findings provide the first comprehensive atlas of functional topology across different phenotypes
173 healthcare resource data from the Dartmouth Atlas of Health Care (2006), and Medicare fee-for-servic
176 magnetic resonance imaging-based human brain atlas of important serotonin receptors and the transport
180 project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 4
181 risation of shellac by HPLC-ESI-Q-ToF and an atlas of MS/MS spectra of shellac components, this work
183 morsphere systems, we generate a large-scale atlas of mutant-IDH1-induced epigenomic reprogramming.
184 el for electromagnetic field simulations, an atlas of peripheral nerves, and a neurodynamic model to
186 way for the construction of a comprehensive atlas of public mouse and human immune repertoires with
187 -specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritabili
191 construction of an unbiased four-dimensional atlas of the developing fetal brain by integrating symme
193 rvival, thereby presenting an in-depth human atlas of the immune tumor microenvironment in this disea
195 has been used to generate a gene expression atlas of the major plant tissues (i.e. leaf, root, stem,
196 uce a single-cell resolution gene expression atlas of the newborn mouse kidney, an interesting time i
198 here is a need for an improved digital brain atlas of the spatiotemporal maturation of the fetal brai
200 An automated method (based on an ex vivo atlas of ultra-high-resolution hippocampal tissue) was u
201 ncers, isomiRs and our resulting 'Pan-cancer Atlas' of isomiR expression could serve as a suitable fr
202 gene expression data from The Cancer Genome Atlas, Oncomine, PrognoScan, and a hepatocellular carcin
205 Eight radiologists from the Cancer Genome Atlas Ovarian Cancer Imaging Research Group developed an
206 PK and HIF-1 signatures to The Cancer Genome Atlas patient transcriptomics data of multiple cancer ty
207 ional concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basi
208 (CTAC), PET with ATAC (air and bone from an atlas), PET with ATACpatientBone (air and tissue from th
210 ol using RNA-seq data from The Cancer Genome Atlas program's Kidney Clear Cell Carcinoma project.
211 ing affinity reagents from the Human Protein Atlas project and multiplexed immuoassays, we extensivel
214 s from two cancer types in the Cancer Genome Atlas project: glioblastoma multiforme and ovarian serou
217 The WHO Child and Adolescent Mental Health Atlas, published in 2005, reported that child and adoles
218 nment procedure to assign functional data to atlas regions and correlate activity between regions to
220 hnique that incorporates two different multi-atlas segmentation propagation and fusion techniques: Th
221 tion with data mining from the Cancer Genome Atlas showed that the neutrophil chemokine CXCL1 gene wa
222 0,737 genes present in the Allen Human Brain Atlas showed the set of top 100 strongest correlating ge
223 ies and real datasets from The Cancer Genome Atlas showed the significant improvement of DMRMark over
224 ains, or groups of related concepts, and our atlas shows which domains are represented in each area.
225 or accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GE
227 n independent cohorts from The Cancer Genome Atlas (TCGA) (n = 414) and EMBL-EBI (n = 53), CLEAR scor
228 ata of ovarian cancer from The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Conso
229 bundance, all available in The Cancer Genome Atlas (TCGA) and developed iDriver, a non-parametric Bay
230 reast cancer patients from The Cancer Genome Atlas (TCGA) and found multiple recurrent gene fusions i
231 ta in 23 cancer types from The Cancer Genome Atlas (TCGA) and identified 1295 mutation clusters.
232 s supported by analysis of The Cancer Genome Atlas (TCGA) and NCBI GEO data sets, which demonstrated
233 SCLC, NSCLC cell lines and The Cancer Genome Atlas (TCGA) and reveal a markedly elevated expression o
234 Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REposi
235 NA expression results from The Cancer Genome Atlas (TCGA) breast cancer data set (n = 1215) to calcul
236 vasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort.
237 CC were identified through The Cancer Genome Atlas (TCGA) clear cell kidney (KIRC) dataset (419 white
239 m a pan-cancer analysis of The Cancer Genome Atlas (TCGA) data set and observe that bi-allelic pathog
242 gene expression data from The Cancer Genome Atlas (TCGA) demonstrate reduced expression of cytotoxic
243 lts were filtered by using The Cancer Genome Atlas (TCGA) expression data in CRC, whereby we generate
244 g RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across 30 cancer types,
246 ulated with data sets from The Cancer Genome Atlas (TCGA) is provided to allow customized query.
247 Compared to a cohort of The Cancer Genome Atlas (TCGA) patients with HER2-positive non-IBC, HER2-p
248 om 26 cancers sequenced in the Cancer Genome Atlas (TCGA) Project to estimate the subset of cancers (
250 Comparison of tumors from The Cancer Genome Atlas (TCGA) reveals that head and neck squamous cell ca
251 adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining
252 10 271 tumor datasets from The Cancer Genome Atlas (TCGA) to evaluate whether isomiRs can distinguish
253 oss eleven cancer types in The Cancer Genome Atlas (TCGA) to identify cancer-predisposing CNV regions
254 estion, 266 melanomas from The Cancer Genome Atlas (TCGA) were categorized by the presence or absence
255 ibus, the Broad Institute, The Cancer Genome Atlas (TCGA), and the European Genome-Phenome Archive.
256 With the completion of The Cancer Genome Atlas (TCGA), there is opportunity for systematic analys
271 pression from the Cancer Genome and Proteome Atlases (TCGA and TCPA) to characterize proteins and pro
275 sue Expression project and The Cancer Genome Atlas to comprehensively analyze the transcriptomes of h
276 analysis on datasets from The Cancer Genome Atlas to elucidate how the expression patterns of mRNAs
277 ers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and different
278 del, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing th
279 d a pan-cancer analysis of The Cancer Genome Atlas to identify transcriptional networks regulated by
280 s possibility, we used data from Allen Brain Atlas to investigate variability in gene expression prof
281 targets and this enabled us to transform the atlas to represent protein densities (in picomoles per m
282 an connectivity research is the use of brain atlases to compare findings across individuals and studi
283 drome, cross-referenced to the Human Protein Atlas, to identify commonly dysregulated pathways and bi
284 ma multiforme samples from The Cancer Genome Atlas using different analysis pipelines, and compared b
286 ted using AAL (Automated Anatomical Labeling atlas) volumes of interest (VOIs) for parietal, temporal
287 ons from the publicly available Digital Hand Atlas was compared with published reports of an existing
288 ng data from 190 tumors in the Cancer Genome Atlas, we correlated immune cell gene expression profile
289 ia database retrieval from The Cancer Genome Atlas, we could highlight the importance of the miR-23a/
290 llen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched i
291 Using the Allen Institute's transcriptional atlas, we further established the colocalization of mu-o
293 em gene expression data from the Allen Brain Atlas, we investigated the impact of transcription facto
294 bioinformatic resource, The Cancer Proteome Atlas, which contains two separate web applications.
295 ain by comparing the 5-HT density across the atlas with data from the Allen Human Brain atlas and ide
297 ith ATACpatientBone (air and tissue from the atlas with patient bone), and PET with ATACboneless (air
298 and genetic studies of a human liver biopsy atlas with the aim of identifying putative therapeutic t
299 cently described [12]; however, combining an atlas with whole-brain calcium imaging has yet to be per
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