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| Status |
Public on Sep 21, 2017 |
| Title |
Analysis of temporal lens gene expression microarrays to expand the eye gene discovery tool iSyTE |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Purpose: While the bioinformatics gene-discovery tool iSyTE (integrated Systems Tool for Eye gene discovery) has proved effective in identifying new cataract-linked genes, it primarily depended on lens-enriched expression of just three wild-type mouse embryonic stages. To increase iSyTE’s efficacy, a broad range of embryonic (E) and postnatal (P) lens microarray datasets from wild-type and specific gene-perturbation mutant mice were analyzed and a new web-interface was developed for their effective access and downstream-analysis.
Methods: Five new mouse lens microarrays were generated and analyzed with all publicly available Affymetrix and Illumina lens datasets representing the stages E9.5, E10.25, E10.5, E11.5, E12.5, E15.5, E16.5, E17.5, E19.5, P0, P2, P4, P8, P12, P20, P28, P30, P42, P52, P56, P60 and mouse mutants for the genes: Brg1, CBP:p300, E2f1:E2f2:E2f3, Foxe3, Hsf4, Klf4, Mafg:Mafk, Notch2, Pax6, Sparc, Tdrd7.
Results: The integrated lens microarray analysis accurately reflects established gene expression patterns and defines a new lens-signature gene-set for embryonic and postnatal stages that includes several novel candidates namely, Grifin, Ogn, Fabp5, Mboat1, Tmem40, Dhx32, Aldoc, Pgam2, Hmgn3, Mocs2, Gprc5b, Gstm1, Npl, and Zbtb8b. Combined analyses of 32 developmental/genetic data-conditions identifies several new transcription and signaling factors that potentially function in lens development and/or homeostasis.
Conclusions: The updated iSyTE web-interface: (1) comprehensively informs on normal lens developmental and cataract-associated transcriptome dynamics and identifies new high-priority candidates for these processes, and (2) offers user-friendly visualization.
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| Overall design |
Microarray comparison of lenses from multiple embryonic and postnatal stages vs. embryonic whole body control and mutant vs. control. This dataset includes lens samples from multiple postnatal stages, and embryonic whole body (minus eye) controls.
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| Contributor(s) |
Lachke SA, Kakrana A, Anand D |
| Citation(s) |
29036527 |
| Submission date |
Jun 16, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Deepti Anand |
| E-mail(s) |
anand@udel.edu
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| Organization name |
University of Delaware
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| Department |
Biological Sciences
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| Street address |
351 Wolf Hall, University of Delaware
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| City |
Newark |
| State/province |
Delaware |
| ZIP/Postal code |
19716 |
| Country |
USA |
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| Platforms (1) |
| GPL6887 |
Illumina MouseWG-6 v2.0 expression beadchip |
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| Samples (12)
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| GSM2671843 |
Developmental time point for iSyTE 2.0 [Lens_P8_A] |
| GSM2671844 |
Developmental time point for iSyTE 2.0 [Lens_P8_B] |
| GSM2671845 |
Developmental time point for iSyTE 2.0 [Lens_P12_A] |
| GSM2671846 |
Developmental time point for iSyTE 2.0 [Lens_P12_B] |
| GSM2671847 |
Developmental time point for iSyTE 2.0 [Lens_P20_A] |
| GSM2671848 |
Developmental time point for iSyTE 2.0 [Lens_P20_B] |
| GSM2671849 |
Developmental time point for iSyTE 2.0 [Lens_P42_A] |
| GSM2671850 |
Developmental time point for iSyTE 2.0 [Lens_P42_B] |
| GSM2671851 |
Developmental time point for iSyTE 2.0 [Lens_P52_A] |
| GSM2671852 |
Developmental time point for iSyTE 2.0 [Lens_P52_B] |
| GSM2671853 |
Whole, embryonic body control for iSyTE 2.0 [WB_10_11_12_A] |
| GSM2671854 |
Whole, embryonic body control for iSyTE 2.0 [WB_10_11_12_B] |
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| Relations |
| BioProject |
PRJNA390783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100136_RAW.tar |
15.8 Mb |
(http)(custom) |
TAR |
| GSE100136_non-normalized.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
| GSE100136_non-normalized_complete_isyte2.txt.gz |
13.1 Mb |
(ftp)(http) |
TXT |
| GSE100136_rankinvariant_bgcorrected_complete.isyte2.txt.gz |
18.1 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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