scholarly journals Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns

2019 ◽  
Author(s):  
Maria Osmala ◽  
Harri Lähdesmäki
Keyword(s):  
Human Genome ◽  
Binding Sites ◽  
State Of The Art ◽  
Regulatory Protein ◽  
Distance Measures ◽  
Supervised Machine Learning ◽  
Cell Type ◽  
Enhancer Prediction ◽  
Art Methods ◽  
Chromatin Feature

AbstractBackgroundThe binding sites of transcription factors (TFs) and the localisation of histone modifications in the human genome can be quantified by the chromatin immunoprecipitation assay coupled with next-generation sequencing (ChIP-seq). The resulting chromatin feature data has been successfully adopted for genome-wide enhancer identification by several unsupervised and supervised machine learning methods. However, the current methods predict different numbers and different sets of enhancers for the same cell type and do not utilise the pattern of the ChIP-seq coverage profiles efficiently.ResultsIn this work, we propose a PRobabilistic Enhancer PRedictIoN Tool (PREPRINT) that assumes characteristic coverage patterns of chromatin features at enhancers and employs a statistical model to account for their variability. PREPRINT defines probabilistic distance measures to quantify the similarity of the genomic query regions and the characteristic coverage patterns. The probabilistic scores of the enhancer and non-enhancer samples are utilised to train a kernel-based classifier. The performance of the method is demonstrated on ENCODE data for two cell lines. The predicted enhancers are computationally validated based on the transcriptional regulatory protein binding sites and compared to the predictions obtained by state-of-the-art methods.ConclusionPREPRINT performs favorably to the state-of-the-art methods, especially when requiring the methods to predict a larger set of enhancers. PREPRINT generalises successfully to data from cell type not utilised for training, and often the PREPRINT performs better than the previous methods. The PREPRINT enhancers are less sensitive to the choice of prediction threshold. PREPRINT identifies biologically validated enhancers not predicted by the competing methods. The enhancers predicted by PREPRINT can aid the genome interpretation in functional genomics and clinical studies.Availabilityhttps://github.com/MariaOsmala/[email protected]

scholarly journals Superscan: Supervised Single-Cell Annotation

2021 ◽  
Author(s):  
Carolyn Shasha ◽  
Yuan Tian ◽  
Florian Mair ◽  
Helen E Rodgers Miller ◽  
Raphael Gottardo
Keyword(s):  
Single Cell ◽  
State Of The Art ◽  
Marker Gene ◽  
Surface Protein ◽  
Cell Types ◽  
Training Data ◽  
Supervised Machine Learning ◽  
Cell Type ◽  
Surface Protein Expression ◽  
Meta Analyses

Automated cell type annotation of single-cell RNA-seq data has the potential to significantly improve and streamline single cell data analysis, facilitating comparisons and meta-analyses. However, many of the current state-of-the-art techniques suffer from limitations, such as reliance on a single reference dataset or marker gene set, or excessive run times for large datasets. Acquiring high-quality labeled data to use as a reference can be challenging. With CITE-seq, surface protein expression of cells can be directly measured in addition to the RNA expression, facilitating cell type annotation. Here, we compiled and annotated a collection of 16 publicly available CITE-seq datasets. This data was then used as training data to develop Superscan, a supervised machine learning-based prediction model. Using our 16 reference datasets, we benchmarked Superscan and showed that it performs better in terms of both accuracy and speed when compared to other state-of-the-art cell annotation methods. Superscan is pre-trained on a collection of primarily PBMC immune datasets; however, additional data and cell types can be easily added to the training data for further improvement. Finally, we used Superscan to reanalyze a previously published dataset, demonstrating its applicability even when the dataset includes cell types that are missing from the training set.

scholarly journals Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans

2020 ◽  
Author(s):  
Pengyu Ni ◽  
Zhengchang Su
Keyword(s):  
Transcription Factor ◽  
Human Genome ◽  
Binding Sites ◽  
State Of The Art ◽  
Accurate Prediction ◽  
Evolutionary Constraints ◽  
Phase 3 ◽  
Regulatory Modules ◽  
Regulatory Genome ◽  
Encode Phase

AbstractAnnotating all cis-regulatory modules (CRMs) and transcription factor (TF) binding sites(TFBSs) in genomes remains challenging. We tackled the task by integrating putative TFBSs motifs found in available 6,092 datasets covering 77.47% of the human genome. This approach enabled us to partition the covered genome regions into a CRM candidate (CRMC) set (56.84%) and a non-CRMC set (43.16%). Intriguingly, like known enhancers, the predicted 1,404,973 CRMCs are under strong evolutionary constraints, suggesting that they might be cis-regulator. In contrast, the non-CRMCs are largely selectively neutral, suggesting that they might not be cis-regulatory. Our method substantially outperforms three state-of-the-art methods (GeneHancers, EnhancerAtlas and ENCODE phase 3) for recalling VISTA enhancers and ClinVar variants, as well as by measurements of evolutionary constraints. We estimated that the human genome might encode about 1.46 million CRMs and 67 million TFBSs, comprising about 55% and 22% of the genome, respectively; for both of which, we predicted 80%. Therefore, the cis-regulatory genome appears to be more prevalent than originally thought.

scholarly journals Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41374 ◽  
Author(s):  
Hebing Chen ◽  
Yao Tian ◽  
Wenjie Shu ◽  
Xiaochen Bo ◽  
Shengqi Wang
Keyword(s):  
Human Genome ◽  
Binding Sites ◽  
Ctcf Binding ◽  
Cell Type ◽  
Cell Type Specific

scholarly journals Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Pengyu Ni ◽  
Zhengchang Su
Keyword(s):  
Binding Sites ◽  
State Of The Art ◽  
Cell Types ◽  
Evolutionary Constraints ◽  
Specific Cell ◽  
Cell Type ◽  
Phase 3 ◽  
Regulatory Modules ◽  
Regulatory Genome ◽  
Encode Phase

Abstract cis-regulatory modules(CRMs) formed by clusters of transcription factor (TF) binding sites (TFBSs) are as important as coding sequences in specifying phenotypes of humans. It is essential to categorize all CRMs and constituent TFBSs in the genome. In contrast to most existing methods that predict CRMs in specific cell types using epigenetic marks, we predict a largely cell type agonistic but more comprehensive map of CRMs and constituent TFBSs in the gnome by integrating all available TF ChIP-seq datasets. Our method is able to partition 77.47% of genome regions covered by available 6092 datasets into a CRM candidate (CRMC) set (56.84%) and a non-CRMC set (43.16%). Intriguingly, the predicted CRMCs are under strong evolutionary constraints, while the non-CRMCs are largely selectively neutral, strongly suggesting that the CRMCs are likely cis-regulatory, while the non-CRMCs are not. Our predicted CRMs are under stronger evolutionary constraints than three state-of-the-art predictions (GeneHancer, EnhancerAtlas and ENCODE phase 3) and substantially outperform them for recalling VISTA enhancers and non-coding ClinVar variants. We estimated that the human genome might encode about 1.47M CRMs and 68M TFBSs, comprising about 55% and 22% of the genome, respectively; for both of which, we predicted 80%. Therefore, the cis-regulatory genome appears to be more prevalent than originally thought.

Osteosarcoma of the jaws: a literature review

2020 ◽  
Vol 16 ◽  
Author(s):  
Francesco Ricotta ◽  
Massimo Bassi ◽  
Nicola Tomasetti ◽  
Angelo Campobassi ◽  
Vincenzo Maiolo ◽  
...  
Keyword(s):  
Treatment Guidelines ◽  
State Of The Art ◽  
Bone Erosion ◽  
Tumor Resection ◽  
Bone Destruction ◽  
Cell Type ◽  
Complete Tumor Resection ◽  
Predominant Cell Type ◽  
Bone Changes ◽  
Complete Tumor

: Osteosarcoma of the jaws (OSJ) is a relatively rare disease, accounting for between 2% and 10% of all cases of osteosarcoma, it is morphologically and radiologically identical to the trunk and extremity variant, but distinct in several crucial aspects. : The lesion is characterized by sarcomatous cells which produces a variable amount of osteoid bone. It arises centrally within the bone and can be subdivided into osteoblastic, chondroblastic and fibroblastic subtype, depending on the predominant cell type. : Radiographically, these tumors display a spectrum of bone changes from well-demarcated borders to lytic bone destruction with indefinite margins and variable cortical bone erosion or, in some cases, images of sclerotic bone. Therapeutic options for OSJ include surgery, chemotherapy and radiotherapy, which are employed according to age of the patient, histological classification and localization of the tumor. Today there is no a general consensus in the treatment guidelines for the OSJ though surgery represents the key of the treatment. The main prognostic factor deeply influencing the patient's prognosis remains the complete tumor resection with negative surgical margins. : The aim of the present review is to describe the state of the art regarding diagnostic and surgical treatment aspects of the primary osteosarcoma of the jaws.

scholarly journals Multi-hop assortativities for network classification

2018 ◽  
Vol 7 (4) ◽  
pp. 603-622 ◽  
Author(s):  
Leonardo Gutiérrez-Gómez ◽  
Jean-Charles Delvenne
Keyword(s):  
Machine Learning ◽  
Scientific Collaboration ◽  
State Of The Art ◽  
Medical Engineering ◽  
Research Field ◽  
Classification Task ◽  
Collaboration Network ◽  
Structural Patterns ◽  
Art Methods

Abstract Several social, medical, engineering and biological challenges rely on discovering the functionality of networks from their structure and node metadata, when it is available. For example, in chemoinformatics one might want to detect whether a molecule is toxic based on structure and atomic types, or discover the research field of a scientific collaboration network. Existing techniques rely on counting or measuring structural patterns that are known to show large variations from network to network, such as the number of triangles, or the assortativity of node metadata. We introduce the concept of multi-hop assortativity, that captures the similarity of the nodes situated at the extremities of a randomly selected path of a given length. We show that multi-hop assortativity unifies various existing concepts and offers a versatile family of ‘fingerprints’ to characterize networks. These fingerprints allow in turn to recover the functionalities of a network, with the help of the machine learning toolbox. Our method is evaluated empirically on established social and chemoinformatic network benchmarks. Results reveal that our assortativity based features are competitive providing highly accurate results often outperforming state of the art methods for the network classification task.

scholarly journals Automatic Detection of Discrimination Actions from Social Images

Electronics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 325
Author(s):  
Zhihao Wu ◽  
Baopeng Zhang ◽  
Tianchen Zhou ◽  
Yan Li ◽  
Jianping Fan
Keyword(s):  
Action Recognition ◽  
State Of The Art ◽  
Automatic Detection ◽  
Experimental Results ◽  
Practical Approach ◽  
Detection And Identification ◽  
Art Methods ◽  
Image Set ◽  
Social Images ◽  
Relationship Identification

In this paper, we developed a practical approach for automatic detection of discrimination actions from social images. Firstly, an image set is established, in which various discrimination actions and relations are manually labeled. To the best of our knowledge, this is the first work to create a dataset for discrimination action recognition and relationship identification. Secondly, a practical approach is developed to achieve automatic detection and identification of discrimination actions and relationships from social images. Thirdly, the task of relationship identification is seamlessly integrated with the task of discrimination action recognition into one single network called the Co-operative Visual Translation Embedding++ network (CVTransE++). We also compared our proposed method with numerous state-of-the-art methods, and our experimental results demonstrated that our proposed methods can significantly outperform state-of-the-art approaches.

scholarly journals A Deep Learning Approach to Predict Autism Spectrum Disorder Using Multisite Resting-State fMRI

2021 ◽  
Vol 11 (8) ◽  
pp. 3636
Author(s):  
Faria Zarin Subah ◽  
Kaushik Deb ◽  
Pranab Kumar Dhar ◽  
Takeshi Koshiba
Keyword(s):  
Autism Spectrum Disorder ◽  
Resting State ◽  
State Of The Art ◽  
Resting State Fmri ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Bootstrap Analysis ◽  
Proposed Model ◽  
Art Methods ◽  
The Mean

Autism spectrum disorder (ASD) is a complex and degenerative neuro-developmental disorder. Most of the existing methods utilize functional magnetic resonance imaging (fMRI) to detect ASD with a very limited dataset which provides high accuracy but results in poor generalization. To overcome this limitation and to enhance the performance of the automated autism diagnosis model, in this paper, we propose an ASD detection model using functional connectivity features of resting-state fMRI data. Our proposed model utilizes two commonly used brain atlases, Craddock 200 (CC200) and Automated Anatomical Labelling (AAL), and two rarely used atlases Bootstrap Analysis of Stable Clusters (BASC) and Power. A deep neural network (DNN) classifier is used to perform the classification task. Simulation results indicate that the proposed model outperforms state-of-the-art methods in terms of accuracy. The mean accuracy of the proposed model was 88%, whereas the mean accuracy of the state-of-the-art methods ranged from 67% to 85%. The sensitivity, F1-score, and area under receiver operating characteristic curve (AUC) score of the proposed model were 90%, 87%, and 96%, respectively. Comparative analysis on various scoring strategies show the superiority of BASC atlas over other aforementioned atlases in classifying ASD and control.

scholarly journals A contour property based approach to segment nuclei in cervical cytology images

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Iram Tazim Hoque ◽  
Nabil Ibtehaz ◽  
Saumitra Chakravarty ◽  
M. Saifur Rahman ◽  
M. Sohel Rahman
Keyword(s):  
Pap Smear ◽  
State Of The Art ◽  
Cervical Cytology ◽  
Average Intensity ◽  
Nucleus Size ◽  
Real Dataset ◽  
Art Methods ◽  
Convolution Filter ◽  
Cervical Cells ◽  
Nucleus Segmentation

Abstract Background Segmentation of nuclei in cervical cytology pap smear images is a crucial stage in automated cervical cancer screening. The task itself is challenging due to the presence of cervical cells with spurious edges, overlapping cells, neutrophils, and artifacts. Methods After the initial preprocessing steps of adaptive thresholding, in our approach, the image passes through a convolution filter to filter out some noise. Then, contours from the resultant image are filtered by their distinctive contour properties followed by a nucleus size recovery procedure based on contour average intensity value. Results We evaluate our method on a public (benchmark) dataset collected from ISBI and also a private real dataset. The results show that our algorithm outperforms other state-of-the-art methods in nucleus segmentation on the ISBI dataset with a precision of 0.978 and recall of 0.933. A promising precision of 0.770 and a formidable recall of 0.886 on the private real dataset indicate that our algorithm can effectively detect and segment nuclei on real cervical cytology images. Tuning various parameters, the precision could be increased to as high as 0.949 with an acceptable decrease of recall to 0.759. Our method also managed an Aggregated Jaccard Index of 0.681 outperforming other state-of-the-art methods on the real dataset. Conclusion We have proposed a contour property-based approach for segmentation of nuclei. Our algorithm has several tunable parameters and is flexible enough to adapt to real practical scenarios and requirements.

Sign in / Sign up

Export Citation Format

Share Document