esATAC Report for Case and Control
Zheng Wei and Wei Zhang
2018-02-14
load("Report2.Rdata")1 Case Control Peak Compare
The following is the peak comparation result for case and control.
The total peaks in case are 116445, specific peaks in case are 51679.
The total peaks in control are 109188, specific peaks in control are 45545.
The overlap peaks are merged to 61229 peaks.
2 GO Analysis
Gene ontology analysis for all genes around specific peak regions of case and control.
2.1 Significant GO terms of genes associated with case specific peaks
| ID | Description | GeneRatio | pvalue | qvalue |
|---|---|---|---|---|
| GO:0061564 | axon development | 388/12754 | 2.22e-43 | 4.63e-40 |
| GO:0045666 | positive regulation of neuron differentiation | 354/12754 | 7.17e-43 | 7.47e-40 |
| GO:0007409 | axonogenesis | 364/12754 | 1.86e-41 | 1.29e-38 |
| GO:0022604 | regulation of cell morphogenesis | 386/12754 | 3.65e-41 | 1.9e-38 |
| GO:0031346 | positive regulation of cell projection organization | 349/12754 | 4.78e-38 | 1.99e-35 |
| GO:0010769 | regulation of cell morphogenesis involved in differentiation | 260/12754 | 5.23e-35 | 1.82e-32 |
| GO:0030900 | forebrain development | 309/12754 | 7.85e-35 | 2.34e-32 |
| GO:0044057 | regulation of system process | 399/12754 | 1.21e-34 | 3.15e-32 |
| GO:0007264 | small GTPase mediated signal transduction | 341/12754 | 1.65e-33 | 3.83e-31 |
| GO:0010976 | positive regulation of neuron projection development | 274/12754 | 3.68e-33 | 7.68e-31 |
| GO:0048568 | embryonic organ development | 382/12754 | 1.08e-31 | 2.05e-29 |
| GO:0048732 | gland development | 346/12754 | 2.94e-31 | 5.1e-29 |
| GO:0001525 | angiogenesis | 356/12754 | 3.74e-31 | 6e-29 |
| GO:0001501 | skeletal system development | 381/12754 | 1.82e-29 | 2.71e-27 |
| GO:0035239 | tube morphogenesis | 328/12754 | 3.37e-29 | 4.69e-27 |
2.2 Significant GO terms of genes associated with control specific peaks
| ID | Description | GeneRatio | pvalue | qvalue |
|---|---|---|---|---|
| GO:0007264 | small GTPase mediated signal transduction | 294/10518 | 2.03e-27 | 5.43e-24 |
| GO:0033674 | positive regulation of kinase activity | 316/10518 | 5.59e-27 | 7.46e-24 |
| GO:0001525 | angiogenesis | 307/10518 | 5.45e-26 | 4.85e-23 |
| GO:0031346 | positive regulation of cell projection organization | 291/10518 | 1.03e-25 | 6.84e-23 |
| GO:2000147 | positive regulation of cell motility | 325/10518 | 1.91e-25 | 1.02e-22 |
| GO:0045860 | positive regulation of protein kinase activity | 291/10518 | 6.34e-25 | 2.82e-22 |
| GO:0030335 | positive regulation of cell migration | 313/10518 | 1.23e-24 | 4.68e-22 |
| GO:0051272 | positive regulation of cellular component movement | 330/10518 | 3.02e-24 | 9.08e-22 |
| GO:0001667 | ameboidal-type cell migration | 247/10518 | 3.06e-24 | 9.08e-22 |
| GO:0044089 | positive regulation of cellular component biogenesis | 327/10518 | 6.28e-24 | 1.67e-21 |
| GO:0051493 | regulation of cytoskeleton organization | 308/10518 | 9.25e-23 | 2.24e-20 |
| GO:0045666 | positive regulation of neuron differentiation | 282/10518 | 1.97e-22 | 4.38e-20 |
| GO:0032870 | cellular response to hormone stimulus | 313/10518 | 2.65e-22 | 5.45e-20 |
| GO:0061564 | axon development | 307/10518 | 6.74e-22 | 1.29e-19 |
| GO:0022604 | regulation of cell morphogenesis | 308/10518 | 7.47e-22 | 1.33e-19 |
3 Motif Enrichment Analysis
This function takes case and control specific peaks as foreground respectively, overlap peaks between case and control as background.
3.1 Significant motifs of case specific peaks
| motif | motif length | p_value |
|---|---|---|
| CTCF | 19 | 9.57e-54 |
3.2 Significant motifs of control specific peaks
| motif | motif length | p_value |
|---|---|---|
| CTCF | 19 | 2.45e-30 |
4 Genomic Footprint
The following is the footprint for motif occurance of case&control peaks.
For all footprint of case sample, The absolute path is /home/zwei/esATAC_test/mm10RepCC/esATAC_pipeline/intermediate_results/case/rep_concord_merge/Footprint_Case_data/FP_PDF_Case_data.
For all footprint of control sample, The absolute path is /home/zwei/esATAC_test/mm10RepCC/esATAC_pipeline/intermediate_results/control/rep_concord_merge/Footprint_Control_data/FP_PDF_Control_data.
The following is the footprint for motif occurance of case&control specific peaks.
For all footprint of case specific, The absolute path is /home/zwei/esATAC_test/mm10RepCC/esATAC_pipeline/intermediate_results/case_control/Footprint_Case_specific/FP_PDF_Case_specific.
For all footprint of control specific, The absolute path is /home/zwei/esATAC_test/mm10RepCC/esATAC_pipeline/intermediate_results/case_control/Footprint_Control_specific/FP_PDF_Control_specific.
5 Session Info
sessionInfo()## R version 3.4.3 (2017-11-30)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.2 (Maipo)
##
## Matrix products: default
## BLAS: /home/software/R/R-3.4.3/lib64/R/lib/libRblas.so
## LAPACK: /home/software/R/R-3.4.3/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
## [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
## [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
## [7] LC_PAPER=en_US.utf8 LC_NAME=en_US.utf8
## [9] LC_ADDRESS=en_US.utf8 LC_TELEPHONE=en_US.utf8
## [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=en_US.utf8
##
## attached base packages:
## [1] grid stats4 parallel methods stats graphics grDevices
## [8] utils datasets base
##
## other attached packages:
## [1] corrplot_0.84
## [2] VennDiagram_1.6.18
## [3] futile.logger_1.4.3
## [4] ChIPseeker_1.14.1
## [5] gridExtra_2.3
## [6] ggplot2_2.2.1
## [7] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0
## [8] GenomicFeatures_1.30.3
## [9] org.Mm.eg.db_3.5.0
## [10] AnnotationDbi_1.40.0
## [11] BSgenome.Mmusculus.UCSC.mm10_1.4.0
## [12] BSgenome_1.46.0
## [13] rtracklayer_1.38.3
## [14] esATAC_1.0.15
## [15] ShortRead_1.36.0
## [16] GenomicAlignments_1.14.1
## [17] SummarizedExperiment_1.8.1
## [18] DelayedArray_0.4.1
## [19] matrixStats_0.53.1
## [20] Biobase_2.38.0
## [21] BiocParallel_1.12.0
## [22] Rsamtools_1.30.0
## [23] Biostrings_2.46.0
## [24] XVector_0.18.0
## [25] GenomicRanges_1.30.1
## [26] GenomeInfoDb_1.14.0
## [27] IRanges_2.12.0
## [28] S4Vectors_0.16.0
## [29] BiocGenerics_0.24.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.1.2
## [2] fastmatch_1.1-0
## [3] VGAM_1.0-5
## [4] plyr_1.8.4
## [5] igraph_1.1.2
## [6] lazyeval_0.2.1
## [7] splines_3.4.3
## [8] gridBase_0.4-7
## [9] TFBSTools_1.16.0
## [10] digest_0.6.15
## [11] BiocInstaller_1.28.0
## [12] htmltools_0.3.6
## [13] GOSemSim_2.4.1
## [14] viridis_0.5.0
## [15] GO.db_3.5.0
## [16] gdata_2.18.0
## [17] magrittr_1.5
## [18] memoise_1.1.0
## [19] JASPAR2016_1.6.0
## [20] readr_1.1.1
## [21] annotate_1.56.1
## [22] R.utils_2.6.0
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## [24] colorspace_1.3-2
## [25] blob_1.1.0
## [26] dplyr_0.7.4
## [27] RCurl_1.95-4.10
## [28] jsonlite_1.5
## [29] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [30] bindr_0.1
## [31] TFMPvalue_0.0.6
## [32] brew_1.0-6
## [33] glue_1.2.0
## [34] gtable_0.2.0
## [35] zlibbioc_1.24.0
## [36] UpSetR_1.3.3
## [37] Rook_1.1-1
## [38] scales_0.5.0
## [39] DOSE_3.4.0
## [40] futile.options_1.0.0
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## [48] htmlwidgets_1.0
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## [50] DiagrammeR_0.9.2
## [51] fgsea_1.4.1
## [52] gplots_3.0.1
## [53] RColorBrewer_1.1-2
## [54] pkgconfig_2.0.1
## [55] XML_3.98-1.9
## [56] rJava_0.9-9
## [57] R.methodsS3_1.7.1
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## [60] reshape2_1.4.3
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## [80] compiler_3.4.3
## [81] rstudioapi_0.7
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## [84] Rbowtie2_1.0.1
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## [106] GenomeInfoDbData_1.0.0
## [107] hms_0.4.1
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## [111] rmarkdown_1.8
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