|
| Status |
Public on Feb 09, 2017 |
| Title |
Temporal profiling and network analysis of rhythmic gene expression and novel functional gene annotation in the water flea, Daphnia pulex |
| Organism |
Daphnia pulex |
| Experiment type |
Expression profiling by array
|
| Summary |
We analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 48 hr time period using a cosine-fitting algorithm. Additionally, using a comprehensive network modeling and analysis approach, we go beyond the standard statistical analyses of the gene expression data. By doing so, we identified novel co-regulated rhythmic genes that have similar network topological as well as functional annotations as rhythmic genes identified by the statistical analyses but that cannot be identified by cosine-fitting alone. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus complementing the current limited functional annotation data. Our results revealed extensive 24 hr rhythms in gene expression patterns.
Moderate longitudinal study of circadian rhythm with twelve 4-hour period measurements collected over the course of 48 hours. See Supplimental Image - Modified Loop Design.png
|
| |
|
| Overall design |
Periodic measures were compared in a nearly saturated modified loop design with N-period time point compared with N+4-hour period time point, followed by N-period time point compared with N+12-hour period time point. The loop is closed with N+4-hour period time point compared with N-period time point and N+12-hour period time point compared with N-period time up to the 3rd cycle.
|
| |
|
| Contributor(s) |
Rund SS, Yoo B, Alam CD, Green T, Stephens MT, Zeng E, Sheppard AD, Duffield GE, Milenković T, Pfrender ME |
| Citation(s) |
27538446 |
| |
| Submission date |
Apr 12, 2015 |
| Last update date |
Feb 11, 2017 |
| Contact name |
Jacqueline Lopez |
| E-mail(s) |
jacqueline.ann.lopez@gmail.com
|
| Phone |
574-631-1902
|
| Organization name |
University of Notre Dame
|
| Department |
Biology
|
| Lab |
Pfrender Laboratory
|
| Street address |
019 Galvin Life Science Center
|
| City |
Notre Dame |
| State/province |
Indiana |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20021 |
NimbleGen Daphnia pulex Expression Array 12x135k (PROBE DESIGN ID) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA280899 |
Less...
More...