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:

Figure 1.

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)
## Platform: x86_64-unknown-linux-gnu (64-bit)
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## attached base packages:
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##  [7] Rsamtools_1.13.24      XML_3.98-1.1           annotate_1.39.0       
## [10] biomaRt_2.17.2         bitops_1.0-5           colorspace_1.2-2      
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## [28] stats4_3.0.1           stringr_0.6.2          survival_2.37-4       
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