Differential motif enrichment analysis of paired ChIP-seq experiments
- Lesluyes, Tom, Johnson, James, Machanick, Philip, Bailey, Timothy L
- Authors: Lesluyes, Tom , Johnson, James , Machanick, Philip , Bailey, Timothy L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439250 , vital:73559 , https://doi.org/10.1186/1471-2164-15-752
- Description: Motif enrichment analysis of transcription factor ChIP-seq data can help identify transcription factors that cooperate or compete. Previously, little attention has been given to comparative motif enrichment analysis of pairs of ChIP-seq experiments, where the binding of the same transcription factor is assayed under different conditions. Such comparative analysis could potentially identify the distinct regulatory partners/competitors of the assayed transcription factor under different conditions or at different stages of development.
- Full Text:
- Date Issued: 2014
- Authors: Lesluyes, Tom , Johnson, James , Machanick, Philip , Bailey, Timothy L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439250 , vital:73559 , https://doi.org/10.1186/1471-2164-15-752
- Description: Motif enrichment analysis of transcription factor ChIP-seq data can help identify transcription factors that cooperate or compete. Previously, little attention has been given to comparative motif enrichment analysis of pairs of ChIP-seq experiments, where the binding of the same transcription factor is assayed under different conditions. Such comparative analysis could potentially identify the distinct regulatory partners/competitors of the assayed transcription factor under different conditions or at different stages of development.
- Full Text:
- Date Issued: 2014
How to establish a bioinformatics postgraduate degree programme—a case study from South Africa
- Machanick, Philip, Tastan Bishop, Özlem
- Authors: Machanick, Philip , Tastan Bishop, Özlem
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124641 , vital:35641 , https://doi.10.1093/bib/bbu014
- Description: The Research Unit in Bioinformatics at Rhodes University (RUBi), South Africa, offers a Masters of Science in Bioinformatics.Growing demand for bioinformatics qualifications results in applications from across Africa.Courses aim to bridge gaps in the diverse backgrounds of students who range from biologists with no prior computing exposure to computer scientists with no biology background. The programme is evenly split between coursework and research, with diverse modules from a range of departments coveringmathematics, statistics, computer science and biology, with emphasis on application to bioinformatics research. The early focus on research helps bring students up to speed with working as a researcher. We measure success of the programme by the high rate of subsequent entry to PhD study: 10 of 14 students who completed in the years 2011-2013.
- Full Text:
- Date Issued: 2014
- Authors: Machanick, Philip , Tastan Bishop, Özlem
- Date: 2014
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124641 , vital:35641 , https://doi.10.1093/bib/bbu014
- Description: The Research Unit in Bioinformatics at Rhodes University (RUBi), South Africa, offers a Masters of Science in Bioinformatics.Growing demand for bioinformatics qualifications results in applications from across Africa.Courses aim to bridge gaps in the diverse backgrounds of students who range from biologists with no prior computing exposure to computer scientists with no biology background. The programme is evenly split between coursework and research, with diverse modules from a range of departments coveringmathematics, statistics, computer science and biology, with emphasis on application to bioinformatics research. The early focus on research helps bring students up to speed with working as a researcher. We measure success of the programme by the high rate of subsequent entry to PhD study: 10 of 14 students who completed in the years 2011-2013.
- Full Text:
- Date Issued: 2014
Preliminary thoughts on services without servers
- Machanick, Philip, Hunt, Kieran
- Authors: Machanick, Philip , Hunt, Kieran
- Date: 2014
- Language: English
- Type: Conference paper
- Identifier: vital:6612 , http://hdl.handle.net/10962/d1014082
- Description: Warehouse-scale computing supports cloud-based services such as shared disk space, computation services and social networks. Although warehouse-scale computing is inexpensive per user, the cost to entry is high, and the pressures to generate revenues to cover costs leads service providers to pursue monetizing services aggressively. In this paper, we explore some ideas for removing the need for central servers by exploiting peer-to-peer technologies.
- Full Text:
- Date Issued: 2014
- Authors: Machanick, Philip , Hunt, Kieran
- Date: 2014
- Language: English
- Type: Conference paper
- Identifier: vital:6612 , http://hdl.handle.net/10962/d1014082
- Description: Warehouse-scale computing supports cloud-based services such as shared disk space, computation services and social networks. Although warehouse-scale computing is inexpensive per user, the cost to entry is high, and the pressures to generate revenues to cover costs leads service providers to pursue monetizing services aggressively. In this paper, we explore some ideas for removing the need for central servers by exploiting peer-to-peer technologies.
- Full Text:
- Date Issued: 2014
Teaching Without Technology
- Authors: Machanick, Philip
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439238 , vital:73558 , https://homes.cs.ru.ac.za/philip/Publications/_SACLA/teachWOtech-2014.pdf
- Description: Technology is touted as a solution to problems in education. But is it? I report here on experiences with dropping use of slides in lectures and returning to working on the board. The apparent result is more interactive, engaged classes. Unfortunately there are too many other variables to make the experiences here definitive. The purpose of this paper is to provoke discussion on whether technology is overused in teaching when the goals of improving student engagement and general effectiveness of learning can be met many ways. Technology is not necessarily bad, but making it the starting point risks locking out nontechnological options.
- Full Text:
- Date Issued: 2014
- Authors: Machanick, Philip
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439238 , vital:73558 , https://homes.cs.ru.ac.za/philip/Publications/_SACLA/teachWOtech-2014.pdf
- Description: Technology is touted as a solution to problems in education. But is it? I report here on experiences with dropping use of slides in lectures and returning to working on the board. The apparent result is more interactive, engaged classes. Unfortunately there are too many other variables to make the experiences here definitive. The purpose of this paper is to provoke discussion on whether technology is overused in teaching when the goals of improving student engagement and general effectiveness of learning can be met many ways. Technology is not necessarily bad, but making it the starting point risks locking out nontechnological options.
- Full Text:
- Date Issued: 2014
Inferring direct DNA binding from ChIP-seq
- Bailey, Timothy L, Machanick, Philip
- Authors: Bailey, Timothy L , Machanick, Philip
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439314 , vital:73565 , https://doi.org/10.1093/nar/gks433
- Description: Genome-wide binding data from transcription factor ChIP-seq experiments is the best source of information for inferring the relative DNA-binding affinity of these proteins in vivo . However, standard motif enrichment analysis and motif discovery approaches sometimes fail to correctly identify the binding motif for the ChIP-ed factor. To overcome this problem, we propose ‘central motif enrichment analysis’ (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. We describe a novel visualization and statistical analysis tool—CentriMo—that identifies the region of maximum central enrichment in a set of ChIP-seq peak regions and displays the positional distributions of predicted sites. Using CentriMo for motif enrichment analysis, we provide evidence that one transcription factor (Nanog) has different binding affinity in vivo than in vitro , that another binds DNA cooperatively (E2f1), and confirm the in vivo affinity of NFIC, rescuing a difficult ChIP-seq data set. In another data set, CentriMo strongly suggests that there is no evidence of direct DNA binding by the ChIP-ed factor (Smad1). CentriMo is now part of the MEME Suite software package available at http://meme.nbcr.net . All data and output files presented here are available at: http://research.imb.uq.edu.au/t.bailey/sd/Bailey2011a .
- Full Text:
- Date Issued: 2012
- Authors: Bailey, Timothy L , Machanick, Philip
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439314 , vital:73565 , https://doi.org/10.1093/nar/gks433
- Description: Genome-wide binding data from transcription factor ChIP-seq experiments is the best source of information for inferring the relative DNA-binding affinity of these proteins in vivo . However, standard motif enrichment analysis and motif discovery approaches sometimes fail to correctly identify the binding motif for the ChIP-ed factor. To overcome this problem, we propose ‘central motif enrichment analysis’ (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. We describe a novel visualization and statistical analysis tool—CentriMo—that identifies the region of maximum central enrichment in a set of ChIP-seq peak regions and displays the positional distributions of predicted sites. Using CentriMo for motif enrichment analysis, we provide evidence that one transcription factor (Nanog) has different binding affinity in vivo than in vitro , that another binds DNA cooperatively (E2f1), and confirm the in vivo affinity of NFIC, rescuing a difficult ChIP-seq data set. In another data set, CentriMo strongly suggests that there is no evidence of direct DNA binding by the ChIP-ed factor (Smad1). CentriMo is now part of the MEME Suite software package available at http://meme.nbcr.net . All data and output files presented here are available at: http://research.imb.uq.edu.au/t.bailey/sd/Bailey2011a .
- Full Text:
- Date Issued: 2012