# Genes with Zelda motif

Author: Jeff Johnston

Date: 2013-07-19 23:30:06

## Background

The transcription factor Zelda was found to bind to “TAGteam” sites and play a role in the zygotic genome activation in Drosophila (Liang et al. 2008 ).

## Overview

In this analysis, we will use Bioconductor (Gentleman et al. 2004 ) tools to identify genes with multiple TAGteam motifs in their promoters and perform a GO analysis on these genes.

## Distribution of Zelda motifs in promoters

As we have 23017 transcripts and 14869 genes, we will select a single transcript per gene using the highest Zelda motif count.

The distribution of genes by Zelda motif count is plotted below:

Zelda_Motif_Count | Number_of_Genes
--- | ---
0 | 7024
1 | 5075
2 | 1992
3 | 547
4 | 185
5 | 31
6 | 12
7 | 3

## GO analysis of genes with multiple Zelda motifs

Based on the above histogram, we will select those genes with at least 4 Zelda motifs and perform GO analysis to identify enriched GO categories using GOstats (Falcon & Gentleman, 2006 ).

Below are the over-represented GO categories among these 231 genes (p < 0.001):

GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term
--- | --- | --- | --- | --- | --- | ---
GO:0006334 | 0.00000 | 12.40 | 2.4 | 22 | 130 | nucleosome assembly
GO:0031497 | 0.00000 | 11.43 | 2.5 | 22 | 139 | chromatin assembly
GO:0034728 | 0.00000 | 11.33 | 2.6 | 22 | 140 | nucleosome organization
GO:0006333 | 0.00000 | 10.96 | 2.6 | 22 | 144 | chromatin assembly or disassembly
GO:0065004 | 0.00000 | 10.36 | 2.8 | 22 | 151 | protein-DNA complex assembly
GO:0071824 | 0.00000 | 9.26 | 3.0 | 22 | 166 | protein-DNA complex subunit organization
GO:0006323 | 0.00000 | 8.54 | 3.2 | 22 | 178 | DNA packaging
GO:0071103 | 0.00000 | 8.06 | 3.4 | 22 | 187 | DNA conformation change
GO:0034622 | 0.00000 | 5.83 | 5.0 | 24 | 274 | cellular macromolecular complex assembly
GO:0065003 | 0.00000 | 5.25 | 5.5 | 24 | 301 | macromolecular complex assembly
GO:0006325 | 0.00000 | 5.35 | 5.1 | 23 | 282 | chromatin organization
GO:0044260 | 0.00000 | 2.37 | 56.3 | 92 | 3088 | cellular macromolecule metabolic process
GO:0043933 | 0.00000 | 3.84 | 8.3 | 27 | 454 | macromolecular complex subunit organization
GO:0051276 | 0.00000 | 3.83 | 7.6 | 25 | 418 | chromosome organization
GO:0006259 | 0.00000 | 3.80 | 7.0 | 23 | 384 | DNA metabolic process
GO:0044237 | 0.00000 | 2.07 | 72.9 | 104 | 4002 | cellular metabolic process
GO:0090304 | 0.00000 | 2.30 | 28.2 | 53 | 1547 | nucleic acid metabolic process
GO:0043170 | 0.00000 | 2.02 | 69.0 | 99 | 3787 | macromolecule metabolic process
GO:1901360 | 0.00000 | 2.15 | 35.3 | 61 | 1938 | organic cyclic compound metabolic process
GO:0046483 | 0.00000 | 2.15 | 34.5 | 60 | 1895 | heterocycle metabolic process
GO:0006139 | 0.00000 | 2.17 | 32.9 | 58 | 1806 | nucleobase-containing compound metabolic process
GO:0006725 | 0.00001 | 2.12 | 34.2 | 59 | 1878 | cellular aromatic compound metabolic process
GO:0044238 | 0.00002 | 1.91 | 80.3 | 108 | 4406 | primary metabolic process
GO:0034641 | 0.00002 | 2.01 | 35.7 | 59 | 1957 | cellular nitrogen compound metabolic process
GO:0022607 | 0.00002 | 2.68 | 11.4 | 27 | 627 | cellular component assembly
GO:0044085 | 0.00004 | 2.54 | 12.5 | 28 | 684 | cellular component biogenesis
GO:0007540 | 0.00006 | 82.18 | 0.1 | 3 | 5 | sex determination, establishment of X:A ratio
GO:0006807 | 0.00007 | 1.90 | 40.4 | 63 | 2215 | nitrogen compound metabolic process
GO:0071704 | 0.00007 | 1.82 | 85.7 | 111 | 4701 | organic substance metabolic process
GO:0048598 | 0.00010 | 3.82 | 3.8 | 13 | 207 | embryonic morphogenesis
GO:0007419 | 0.00026 | 10.24 | 0.6 | 5 | 32 | ventral cord development
GO:0007538 | 0.00027 | 15.72 | 0.3 | 4 | 18 | primary sex determination
GO:0010565 | 0.00033 | Inf | 0.0 | 2 | 2 | regulation of cellular ketone metabolic process
GO:0016331 | 0.00060 | 4.65 | 1.9 | 8 | 104 | morphogenesis of embryonic epithelium
GO:0045893 | 0.00060 | 3.31 | 4.0 | 12 | 217 | positive regulation of transcription, DNA-dependent
GO:0045944 | 0.00064 | 3.77 | 2.9 | 10 | 159 | positive regulation of transcription from RNA polymerase II promoter
GO:0016348 | 0.00065 | 23.47 | 0.2 | 3 | 10 | imaginal disc-derived leg joint morphogenesis
GO:0036022 | 0.00065 | 23.47 | 0.2 | 3 | 10 | limb joint morphogenesis
GO:0031325 | 0.00072 | 2.81 | 5.8 | 15 | 319 | positive regulation of cellular metabolic process
GO:0010628 | 0.00077 | 3.21 | 4.1 | 12 | 223 | positive regulation of gene expression
GO:0010604 | 0.00083 | 2.88 | 5.3 | 14 | 290 | positive regulation of macromolecule metabolic process
GO:0040034 | 0.00088 | 20.53 | 0.2 | 3 | 11 | regulation of development, heterochronic
GO:0009893 | 0.00089 | 2.75 | 5.9 | 15 | 326 | positive regulation of metabolic process
GO:0048522 | 0.00094 | 2.26 | 10.7 | 22 | 585 | positive regulation of cellular process
GO:0051254 | 0.00097 | 3.12 | 4.2 | 12 | 229 | positive regulation of RNA metabolic process

## References

- S. Falcon, R. Gentleman, (2006) Using Gostats to Test Gene Lists For go Term Association. Bioinformatics 23 257-258 10.1093/bioinformatics/btl567
- Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean YH Yang, Jianhua Zhang, (2004) Unknown. Genome Biology 5 R80-NA 10.1186/gb-2004-5-10-r80
- Hsiao-Lan Liang, Chung-Yi Nien, Hsiao-Yun Liu, Mark M. Metzstein, Nikolai Kirov, Christine Rushlow, (2008) The Zinc-Finger Protein Zelda is A Key Activator of The Early Zygotic Genome in Drosophila. Nature 456 400-403 10.1038/nature07388

## Session info

    ## R version 3.0.1 Patched (2013-07-10 r63263)
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