Next-generation sequencing data format and visualization with ngs.plot 2015Li Shen
An introduction to the commonly used formats for the next-generation sequencing data. ngs.plot is a popular tool for the visualization and data mining of the NGS data.
The quality of data is very important for various downstream analyses, such as sequence assembly, single nucleotide polymorphisms identification this ppt show parameters for
NGS Data quality check and Dataformat of top sequencing machine
Next-generation sequencing data format and visualization with ngs.plot 2015Li Shen
An introduction to the commonly used formats for the next-generation sequencing data. ngs.plot is a popular tool for the visualization and data mining of the NGS data.
The quality of data is very important for various downstream analyses, such as sequence assembly, single nucleotide polymorphisms identification this ppt show parameters for
NGS Data quality check and Dataformat of top sequencing machine
Course: Bioinformatics for Biomedical Research (2014).
Session: 4.1- Introduction to RNA-seq and RNA-seq Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
An update version of the genome assembly including the mention of techniques such as HiC and Bionano. Also include the QC. These are the same slides used in the course for the UNL in Argentina.
Knowing Your NGS Upstream: Alignment and VariantsGolden Helix Inc
Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output.
This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
In this lecture tried to introduce some basic methods of DNA sequencing like pyrosequencing, sequencing by ligation, sequencing by synthesis and Ion Semiconductor Sequencing
and describe them. Also introduced some new sequencing method (third generation sequencing) like SMRT (Single Molecule Real-Time Sequencing) and GridION.
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
Get more information:
http://imdevsoftware.wordpress.com/2014/10/11/2014-metabolomic-data-analysis-and-visualization-workshop-and-tutorials/
Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center.
Similar to last year, I’ve posted all the content (lectures, labs and software) for any one to follow along with at their own pace. I also plan to release videos for all the lectures and labs.
Course: Bioinformatics for Biomedical Research (2014).
Session: 4.1- Introduction to RNA-seq and RNA-seq Data Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
An update version of the genome assembly including the mention of techniques such as HiC and Bionano. Also include the QC. These are the same slides used in the course for the UNL in Argentina.
Knowing Your NGS Upstream: Alignment and VariantsGolden Helix Inc
Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output.
This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
In this lecture tried to introduce some basic methods of DNA sequencing like pyrosequencing, sequencing by ligation, sequencing by synthesis and Ion Semiconductor Sequencing
and describe them. Also introduced some new sequencing method (third generation sequencing) like SMRT (Single Molecule Real-Time Sequencing) and GridION.
Metabolomic Data Analysis Workshop and Tutorials (2014)Dmitry Grapov
Get more information:
http://imdevsoftware.wordpress.com/2014/10/11/2014-metabolomic-data-analysis-and-visualization-workshop-and-tutorials/
Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center.
Similar to last year, I’ve posted all the content (lectures, labs and software) for any one to follow along with at their own pace. I also plan to release videos for all the lectures and labs.
BPSO&1-NN algorithm-based variable selection for power system stability ident...IJAEMSJORNAL
Due to the very high nonlinearity of the power system, traditional analytical methods take a lot of time to solve, causing delay in decision-making. Therefore, quickly detecting power system instability helps the control system to make timely decisions become the key factor to ensure stable operation of the power system. Power system stability identification encounters large data set size problem. The need is to select representative variables as input variables for the identifier. This paper proposes to apply wrapper method to select variables. In which, Binary Particle Swarm Optimization (BPSO) algorithm combines with K-NN (K=1) identifier to search for good set of variables. It is named BPSO&1-NN. Test results on IEEE 39-bus diagram show that the proposed method achieves the goal of reducing variables with high accuracy.
Aplicacion de la metodologia DEA en stata, Aplicacion de la metodologia DEA en stata, Aplicacion de la metodologia DEA en stata, Aplicacion de la metodologia DEA en stata.
Among many data clustering approaches available today, mixed data set of numeric and category data
poses a significant challenge due to difficulty of an appropriate choice and employment of
distance/similarity functions for clustering and its verification. Unsupervised learning models for
artificial neural network offers an alternate means for data clustering and analysis. The objective of this
study is to highlight an approach and its associated considerations for mixed data set clustering with
Adaptive Resonance Theory 2 (ART-2) artificial neural network model and subsequent validation of the
clusters with dimensionality reduction using Autoencoder neural network model.
Dimensionality Reduction and feature extraction.pptxSivam Chinna
Dimensionality reduction, or dimension reduction, is the transformation of data from a high-dimensional space into a low-dimensional space so that the low-dimensional representation retains some meaningful properties of the original data, ideally close to its intrinsic dimension.
Ijricit 01-002 enhanced replica detection in short time for large data setsIjripublishers Ijri
Similarity check of real world entities is a necessary factor in these days which is named as Data Replica Detection.
Time is an critical factor today in tracking Data Replica Detection for large data sets, without having impact over quality
of Dataset. In this we primarily introduce two Data Replica Detection algorithms , where in these contribute enhanced
procedural standards in finding Data Replication at limited execution periods.This contribute better improvised state
of time than conventional techniques . We propose two Data Replica Detection algorithms namely progressive sorted
neighborhood method (PSNM), which performs best on small and almost clean datasets, and progressive blocking (PB),
which performs best on large and very grimy datasets. Both enhance the efficiency of duplicate detection even on very
large datasets.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Investigating the 3D structure of the genome with Hi-C data analysis
1. Investigating the 3D structure of the genome with
Hi-C data analysis
Sylvain Foissac & Nathalie Villa-Vialaneix
prenom.nom@inra.fr
Séminaire MIAT - Toulouse, 2 juin 2017
SF & NV2 | Hi-C data analysis 1/28
2. Sommaire
1 Normalization
2 TAD identification
3 A/B compartments
4 Differential analysis
SF & NV2 | Hi-C data analysis 2/28
3. Sommaire
1 Normalization
2 TAD identification
3 A/B compartments
4 Differential analysis
SF & NV2 | Hi-C data analysis 3/28
4. Purpose of normalization
1 within matrix normalization: make bins comparable within a matrix
(not needed for differential analysis)
SF & NV2 | Hi-C data analysis 4/28
5. Purpose of normalization
1 within matrix normalization: make bins comparable within a matrix
(not needed for differential analysis)
2 between matrix normalization: make the same bin pair comparable
between two matrices (needed for differential analysis)
SF & NV2 | Hi-C data analysis 4/28
6. Different within matrix normalizations
to correct technical biases
(GC content, mappability...)
explicit correction [Yaffe and Tanay, 2011, Hu et al., 2012]: every factor
causing bais is identified and estimated
SF & NV2 | Hi-C data analysis 5/28
7. Different within matrix normalizations
to correct technical biases
(GC content, mappability...)
explicit correction [Yaffe and Tanay, 2011, Hu et al., 2012]: every factor
causing bais is identified and estimated
non parametric correction ICE correction using matrix balancing
[Imakaev et al., 2012]
K = b Kb for a K st ∀ i = 1, . . . , p,
p
j=1
Kij is constant
SF & NV2 | Hi-C data analysis 5/28
8. Different within matrix normalizations
to correct technical biases
picture from [Schmitt et al., 2016]
SF & NV2 | Hi-C data analysis 5/28
9. Different within matrix normalizations
to take distances into account
theoretical distribution taken from [Belton et al., 2012]
Kd
ij =
Kij − Kd(i,j)
σ(Dd(i,j))
with
Kd average counts at distance d
σ(Dd) standard deviation
available in HiTC [Servant et al., 2012]
SF & NV2 | Hi-C data analysis 6/28
10. Between matrix normalization
correct for differences in sequencing depth
standard approach: similar to RNA-seq normalization
SF & NV2 | Hi-C data analysis 7/28
11. Between matrix normalization
correct for differences in sequencing depth
standard approach: similar to RNA-seq normalization
However...
SF & NV2 | Hi-C data analysis 7/28
12. Between matrix normalization
correct for differences in sequencing depth
standard approach: similar to RNA-seq normalization
However...
density adjustment by LOESS fit [Robinson and Oshlack, 2010]
(implemented in csaw)
SF & NV2 | Hi-C data analysis 7/28
13. Sommaire
1 Normalization
2 TAD identification
3 A/B compartments
4 Differential analysis
SF & NV2 | Hi-C data analysis 8/28
15. TAD method jungle
Directionality index [Dixon et al., 2012]: compute divergence between
up/downstream interaction counts + HMM to identify TADs
SF & NV2 | Hi-C data analysis 10/28
16. TAD method jungle
Directionality index [Dixon et al., 2012]: compute divergence between
up/downstream interaction counts + HMM to identify TADs
armatus [Filippova et al., 2013]: maximize a criteria which evaluate a
within/between count ratio + combine multi-resolution results in a
consensual segmentation
SF & NV2 | Hi-C data analysis 10/28
17. TAD method jungle
Directionality index [Dixon et al., 2012]: compute divergence between
up/downstream interaction counts + HMM to identify TADs
armatus [Filippova et al., 2013]: maximize a criteria which evaluate a
within/between count ratio + combine multi-resolution results in a
consensual segmentation
segmentation method [Brault et al., 2017]: block boundary estimation in
matrix
SF & NV2 | Hi-C data analysis 10/28
18. TAD method jungle
Directionality index [Dixon et al., 2012]: compute divergence between
up/downstream interaction counts + HMM to identify TADs
armatus [Filippova et al., 2013]: maximize a criteria which evaluate a
within/between count ratio + combine multi-resolution results in a
consensual segmentation
segmentation method [Brault et al., 2017]: block boundary estimation in
matrix
... (many others), interestingly, very few provides a hierarchical
clustering
Comparisons in: [Fotuhi Siahpirani et al., 2016, Dali and Blanchette, 2017]
SF & NV2 | Hi-C data analysis 10/28
19. DI evolution with respect to armatus TADs
SF & NV2 | Hi-C data analysis 11/28
20. CTCF at TAD boundaries
SF & NV2 | Hi-C data analysis 12/28
21. Enrichment of genomic features around TAD boundaries
Homo Sapiens [Dixon et al., 2012]
Sus Scrofa (PORCINET project)
SF & NV2 | Hi-C data analysis 13/28
22. Current methodological development
Constrained HAC as a way to compare/combine TADs between samples
Contrained HAC: Hierarchical clustering with contiguity constrains
SF & NV2 | Hi-C data analysis 14/28
23. Current methodological development
Constrained HAC as a way to compare/combine TADs between samples
Contrained HAC: Hierarchical clustering with contiguity constrains
Challenges (currently under development with Pierre Neuvial and Marie
Chavent):
methodological issues: what happens when using Ward’s linkage
criterion with a non Euclidean similarity (counts of the Hi-C matrix)?
what happens when adding constrains to HAC? (partially solved)
development of the R package adjclust (Google Summer of Code
selected project)
SF & NV2 | Hi-C data analysis 14/28
24. Sommaire
1 Normalization
2 TAD identification
3 A/B compartments
4 Differential analysis
SF & NV2 | Hi-C data analysis 15/28
25. A/B compartments
[Lieberman-Aiden et al., 2009]
[Giorgetti et al., 2013]
Method (in theory):
compute Pearson correlations between bins
(using interaction counts with all the other bins
of the same chromosome)
compute eigenvectors (or perform PCA) on this
correlation matrix
affect A/B compartments to +/- values of PCs
SF & NV2 | Hi-C data analysis 16/28
26. A/B compartments in practice
after ICED and distance-based normalizations
SF & NV2 | Hi-C data analysis 17/28
27. A/B compartments in practice
after ICED and distance-based normalizations
Method:
differentiate between A/B using sign of the correlation between PCs
and diagonal counts
choose a relevant PC and method maximizing − log10(p − value)
between diagonal counts in +/- PC (2-group comparison Student test)
SF & NV2 | Hi-C data analysis 17/28
29. Sommaire
1 Normalization
2 TAD identification
3 A/B compartments
4 Differential analysis
SF & NV2 | Hi-C data analysis 19/28
30. Filtering
In differential analysis of sequencing data, filtering is a crucial step:
removing low count features (that are little or no chance to be found
differential) improves the test power (leverage the multiple testing
correction effect) and can save unnecessary computational time
SF & NV2 | Hi-C data analysis 20/28
31. Filtering
In differential analysis of sequencing data, filtering is a crucial step:
removing low count features (that are little or no chance to be found
differential) improves the test power (leverage the multiple testing
correction effect) and can save unnecessary computational time
can be performed 1/ at the beginning of the analysis or after the
estimation of the parameters of the model used for differential
analysis
SF & NV2 | Hi-C data analysis 20/28
32. Filtering
In differential analysis of sequencing data, filtering is a crucial step:
removing low count features (that are little or no chance to be found
differential) improves the test power (leverage the multiple testing
correction effect) and can save unnecessary computational time
can be performed 1/ at the beginning of the analysis or after the
estimation of the parameters of the model used for differential
analysis; 2/ can be fixed to an arbitrary value (minimum total count
per sample) or automated from the data
SF & NV2 | Hi-C data analysis 20/28
33. Filtering
In differential analysis of sequencing data, filtering is a crucial step:
removing low count features (that are little or no chance to be found
differential) improves the test power (leverage the multiple testing
correction effect) and can save unnecessary computational time
can be performed 1/ at the beginning of the analysis or after the
estimation of the parameters of the model used for differential
analysis; 2/ can be fixed to an arbitrary value (minimum total count
per sample) or automated from the data
for Hi-C data:
filtering was performed at the beginning of the analysis (to limit the
computation burden)
was performed by using an arbitrary threshold or a threshold based
on the estimation of the noise background by a quantile of
inter-chromosomal counts (as in R package diffHic)
SF & NV2 | Hi-C data analysis 20/28
34. Filtering
In differential analysis of sequencing data, filtering is a crucial step:
removing low count features (that are little or no chance to be found
differential) improves the test power (leverage the multiple testing
correction effect) and can save unnecessary computational time
can be performed 1/ at the beginning of the analysis or after the
estimation of the parameters of the model used for differential
analysis; 2/ can be fixed to an arbitrary value (minimum total count
per sample) or automated from the data
500 kb - automatic filter (filters counts<∼ 5) - 96.4% of pairs filtered out
before filtering after filtering
SF & NV2 | Hi-C data analysis 20/28
35. Exploratory analysis (500kb bins)
chromosome 1
1 0.911
1
0.8886
0.8866
1
0.8566
0.8651
0.8288
1
0.8973
0.9118
0.8912
0.8692
1
0.8935
0.9032
0.8818
0.8799
0.906
1
LW90−160216−GCCAAT
LW90−160223−CTTGTA
LW90−160308−AGTTCC
LW110−160307−CGATGT
LW110−160308−AGTCAA
LW110−160517−ACAGTG
LW
90−160216−G
C
C
AAT
LW
90−160223−C
TTG
TA
LW
90−160308−AG
TTC
C
LW
110−160307−C
G
ATG
T
LW
110−160308−AG
TC
AA
LW
110−160517−AC
AG
TG
−1.0 −0.5 0.0 0.5 1.0
Cosinus (Frobenius norm)
good reproducibility between
experiments
no clear organization with respect to
the condition
SF & NV2 | Hi-C data analysis 21/28
36. Exploratory analysis (500kb bins)
chromosome 1
1 0.911
1
0.8886
0.8866
1
0.8566
0.8651
0.8288
1
0.8973
0.9118
0.8912
0.8692
1
0.8935
0.9032
0.8818
0.8799
0.906
1
LW90−160216−GCCAAT
LW90−160223−CTTGTA
LW90−160308−AGTTCC
LW110−160307−CGATGT
LW110−160308−AGTCAA
LW110−160517−ACAGTG
LW
90−160216−G
C
C
AAT
LW
90−160223−C
TTG
TA
LW
90−160308−AG
TTC
C
LW
110−160307−C
G
ATG
T
LW
110−160308−AG
TC
AA
LW
110−160517−AC
AG
TG
−1.0 −0.5 0.0 0.5 1.0
Cosinus (Frobenius norm)
good reproducibility between
experiments
no clear organization with respect to
the condition
all data after filtering and between
matrix normalization (LOESS)
2 outliers but PC1 is organized with
respect to the condition
SF & NV2 | Hi-C data analysis 21/28
37. Methods for differential analysis of Hi-C
Similar to RNA-seq [Lun and Smyth, 2015] and R package diffHic
(essentially a wrapper for edgeR):
count data modeled by Binomial Negative distribution
SF & NV2 | Hi-C data analysis 22/28
38. Methods for differential analysis of Hi-C
Similar to RNA-seq [Lun and Smyth, 2015] and R package diffHic
(essentially a wrapper for edgeR):
count data modeled by Binomial Negative distribution
parameters (mean, variance per gene) are estimated from data: a
variance vs mean relationship is modeled
SF & NV2 | Hi-C data analysis 22/28
39. Methods for differential analysis of Hi-C
Similar to RNA-seq [Lun and Smyth, 2015] and R package diffHic
(essentially a wrapper for edgeR):
count data modeled by Binomial Negative distribution
parameters (mean, variance per gene) are estimated from data: a
variance vs mean relationship is modeled
test is performed using an exact test (similar to Fisher) or a
log-likelihood ratio test (GLM model)
SF & NV2 | Hi-C data analysis 22/28
40. Complementary remarks about DE analysis
Hi-C data contain more zeros than RNA-seq data: some people
propose to use Zero Inflated BN distribution (unpublished as far as I
know)
SF & NV2 | Hi-C data analysis 23/28
41. Complementary remarks about DE analysis
Hi-C data contain more zeros than RNA-seq data: some people
propose to use Zero Inflated BN distribution (unpublished as far as I
know)
provides a p-value for every pair of bins:
analysis based on a very large number of bins for finer resolutions
(500kb after filtering: 998 623 pairs of bins; without filtering:
13 509 221 pairs of bins): problem solved for 500kb bins but still under
study for 40kb bins
SF & NV2 | Hi-C data analysis 23/28
42. Complementary remarks about DE analysis
Hi-C data contain more zeros than RNA-seq data: some people
propose to use Zero Inflated BN distribution (unpublished as far as I
know)
provides a p-value for every pair of bins:
analysis based on a very large number of bins for finer resolutions
(500kb after filtering: 998 623 pairs of bins; without filtering:
13 509 221 pairs of bins): problem solved for 500kb bins but still under
study for 40kb bins
tests are performed as if bin pairs were independant whereas they are
spatially correlated
SF & NV2 | Hi-C data analysis 23/28
43. Complementary remarks about DE analysis
Hi-C data contain more zeros than RNA-seq data: some people
propose to use Zero Inflated BN distribution (unpublished as far as I
know)
provides a p-value for every pair of bins:
analysis based on a very large number of bins for finer resolutions
(500kb after filtering: 998 623 pairs of bins; without filtering:
13 509 221 pairs of bins): problem solved for 500kb bins but still under
study for 40kb bins
tests are performed as if bin pairs were independant whereas they are
spatially correlated: estimation of model parameters might be improved
if 1/ smoothed with respect to spatial proximity (similar to what is
sometimes performed methylation data analysis); 2/ performed
independantly for pairs of bins at a given distance (future work).
post-analysis of spatial distribution of p-values, work-in-progress with
Pierre Neuvial (submitted CNRS project)
SF & NV2 | Hi-C data analysis 23/28
44. because last page had no picture
probably not suited for the youngest
SF & NV2 | Hi-C data analysis 24/28
45. Preliminary results
913 bin pairs found differential (after multiple testing correction)
most of them are related to 3 chromosomes
parameter setting (filters...) and biological analysis are work-in-progress...
SF & NV2 | Hi-C data analysis 25/28
46. Differential TADs (state-of-the-art)
Detecting differential domains between the two conditions
Existing approaches:
[Fraser et al., 2015] (3 conditions, no replicate)
HMM on TAD boundaries (with a tolerance threshold) to identify
different TAD boundaries between samples
HAC on TADs, cophenetic distance to obtain local conserved structure
by using a z-score approach
SF & NV2 | Hi-C data analysis 26/28
47. Differential TADs (state-of-the-art)
Detecting differential domains between the two conditions
Existing approaches:
[Fraser et al., 2015] (3 conditions, no replicate)
HMM on TAD boundaries (with a tolerance threshold) to identify
different TAD boundaries between samples
HAC on TADs, cophenetic distance to obtain local conserved structure
by using a z-score approach
R package diffHic computes up/down-stream counts (with ± 100Kb)
and uses the GLM model implemented in edgeR with an interaction
between stream direction (up/down) and condition.
SF & NV2 | Hi-C data analysis 26/28
48. Differential TADs (state-of-the-art)
Detecting differential domains between the two conditions
Existing approaches:
[Fraser et al., 2015] (3 conditions, no replicate)
HMM on TAD boundaries (with a tolerance threshold) to identify
different TAD boundaries between samples
HAC on TADs, cophenetic distance to obtain local conserved structure
by using a z-score approach
R package diffHic computes up/down-stream counts (with ± 100Kb)
and uses the GLM model implemented in edgeR with an interaction
between stream direction (up/down) and condition.
However, the first approach does not take biological variability into account
(no replicate) and the second uses only a very aggregated criterion.
SF & NV2 | Hi-C data analysis 26/28
49. Differential TADs (perspectives)
Ideas for future work
Using constrained HAC, are we able to:
compute a consensus dendrogram using several biological replicates;
differentiate branches significantly (in which sense?) different
between conditions taking into account the within condition variability?
SF & NV2 | Hi-C data analysis 27/28
50. Differential TADs (perspectives)
Ideas for future work
Using constrained HAC, are we able to:
compute a consensus dendrogram using several biological replicates;
differentiate branches significantly (in which sense?) different
between conditions taking into account the within condition variability?
SF & NV2 | Hi-C data analysis 27/28
51. Conclusions and perspectives
Honnestly, it’s late and I really do not believe that I will have enough time to
make a conclusion and discuss perspectives so...
Questions?
SF & NV2 | Hi-C data analysis 28/28
52. References
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Efficient block boundaries estimation in block-wise constant matrices: an application to HiC data.
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Dali, R. and Blanchette, M. (2017).
A critical assessment of topologically associating domain prediction tools.
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SF & NV2 | Hi-C data analysis 28/28
53. Genome Biology, 14:142.
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Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
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Dekker, J. (2009).
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A 3D map of the human genome at kilobase resolution reveals principle of chromatin looping.
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Robinson, M. and Oshlack, A. (2010).
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Servant, N., Lajoie, B., Nora, E., Giorgetti, L., Chen, C., Heard, E., Dekker, J., and Barillot, E. (2012).
SF & NV2 | Hi-C data analysis 28/28
54. HiTC: exploration of high-throughput ‘C’ experiments.
Bioinformatics, 28(21):2843–2844.
Yaffe, E. and Tanay, A. (2011).
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.
Nature Genetics, 43:1059–1065.
SF & NV2 | Hi-C data analysis 28/28