Table 1. Differentially expressed genes of interest from Hoxa1 microarray.
Twelve candidate genes were selected from the list of down-regulated genes and seven from the list of up-regulated genes, based on their published expression pattern and proposed function during development. Candidates were analyzed further by quantitative PCR and/or in situ hybridization. Genes highlighted in green and red were confirmed to be down- or up-regulated, respectively. FC, fold change.
| Gene | FC | Gene name | Proposed function | Expression |
|---|---|---|---|---|
| Dfna5 | 6.0 | Deafness, autosomal dominant 5 | inner ear receptor cell differentiation | E10.5 (northern) |
| Foxd3 | 4.8 | Forkhead box D3 | maintenance/induction of NCC | E9.5, pre-migratory NCC |
| Lhx5 | 4.5 | LIM homeobox protein 5 | respiration (reticulospinal), cardiac dev. | E10.5 |
| Sema3c | 3.0 | Semaphorin 3c | NCC, nervous system, heart dev. | E10.5, cardiac OT |
| Hnf1b | 2.8 | HNF1 homeobox b | hindbrain r5 dev., NCC | E8.0, hindbrain, NCC, foregut |
| Spry4 | 2.6 | Sprouty 4 | Fgf signaling, craniofacial dev. | E8.5, lateral to hindbrain |
| Fzd8 | 2.5 | Frizzled 8 | Wnt receptor | E8.5, head, otic placode |
| Wnt10b | 2.4 | Wingless related 10b | Wnt signaling | E11, 1st arch |
| Tbx15 | 2.4 | T-box 15 | craniofacial dev. | E11, CNS |
| Pax8 | 2.3 | Paired box gene 8 | inner ear (otic placode specification) | ≥ 0ss, otic placode |
| Zic1 | 2.3 | Zinc finger protein of the cerebellum 1 | neural plate patterning, NC specification | ≥ 6ss, hindbrain, neural tube |
| Hoxd3 | 2.1 | Homeobox d3 | cervical vertebrae dev., postnatal death | E9, hindbrain r4/r5 border |
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| ||||
| Apob | 6.8 | Apolipoprotein B | artery morphogenesis | E7.5 (RT-PCR) |
| Clic5 | 5.7 | Chloride intracellular channel 5 | auditory receptor cell organization | E16.5, cochlea |
| Lefty1 | 2.8 | Left right determination factor 1 | left-right patterning | 3–6ss, floor plate |
| Nodal | 2.7 | Nodal | left-right patterning | 3–5ss, node, mesoderm |
| Hnf4a | 2.7 | Hepatic nuclear factor 4a | endodermal organ development | E8.5, fore-midgut endoderm |
| Fgfr3 | 2.5 | Fibroblast growth factor receptor 3 | inner ear dev. (hearing loss in humans) | E9.0, otic placode |
| Lefty2 | 2.3 | Left right determination factor 2 | left-right patterning | 3–6ss, mesoderm |
Nineteen genes were selected from the total list of 299 differentially expressed genes for further analysis by RT- and qPCR, based on their expression pattern and/or proposed function during development as deduced from the Mouse Genome Informatics webpage (http://www.informatics.jax.org/). Genes highlighted in green or red were confirmed to be down- or up-regulated. FC, fold change.