Comb-p
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TL;DR: This work provides validation and example uses on bisulfite-seq with P-values from Fisher's exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics.
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Abstract: Summary:comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher’s exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications.
Availability:comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues.
Contact: bpederse@gmail.com
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References
The Human Genome Browser at UCSC
W. James Kent,Charles W. Sugnet,Terrence S. Furey,Krishna M. Roskin,Tom H. Pringle,Alan M. Zahler,and David Haussler +6 more
TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
Rectangular Confidence Regions for the Means of Multivariate Normal Distributions
TL;DR: For rectangular confidence regions for the mean values of multivariate normal distributions, this paper proved that a confidence region constructed for independent coordinates is, at the same time, a conservative confidence region for any case of dependent coordinates.
2.6K
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
Rafael A. Irizarry,Christine Ladd-Acosta,Bo Wen,Zhijin Wu,Carolina Montano,Patrick Onyango,Hengmi Cui,Kevin Gabo,Michael Rongione,Maree J. Webster,Hong-Fei Ji,James B. Potash,Sarven Sabunciyan,Andrew P. Feinberg +13 more
TL;DR: Methylation changes in cancer are at sites that vary normally in tissue differentiation, consistent with the epigenetic progenitor model of cancer, which proposes that epigenetic alterations affecting tissue-specific differentiation are the predominant mechanism by which epigenetic changes cause cancer.
Genome-Wide Demethylation of Arabidopsis Endosperm
Tzung-Fu Hsieh,Christian A. Ibarra,Pedro Silva,Assaf Zemach,Leor Eshed-Williams,Robert L. Fischer,Daniel Zilberman +6 more
TL;DR: Almost the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences, indicating that CG demethylation is specific to maternal sequences.
Truncated product method for combining P‐values
TL;DR: A new procedure to take the product of only those P‐values less than some specified cut‐off value and to evaluate the probability of such a product, or a smaller value, under the overall hypothesis that all L hypotheses are true is presented.