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Table 2 Neural-specific mRNA decay analysis: functional annotation of high-stability and low-stability mRNAs

From: Dynamic regulation of mRNA decay during neural development

Neural-specific measurements: low-stability mRNAs

GO term

Definition

P value

FDR

Count

Fold enrichment

0006351

Transcription

4 × 10−10

2 × 10−7

58

2.5

 

svp, dpn, pros, vvl, grh, gsb, onecut

    

0030182

Neuron differentiation

2 × 10−7

4 × 10−5

48

2.3

 

chinmo, Dl, tup, Ephrin, Eph, fax, shot

    

0007067

Mitosis

6 × 10−5

3 × 10−3

21

2.9

 

cycB3, cdc27, Sse, cnn, glu, mts

    

0018024

Histone methyltransferase activity

2 × 10−4

.02

7

6.9

 

G9a, Set1, Set2, Su(z)12, ash1, egg

    

0006897

Endocytosis

4 × 10−3

.08

25

1.9

 

Arpc4, shi, CalpA, pat1, faf, scb, Rac1

    

0005840

Ribosome

2 × 10−3

.06

21

2.0

 

RpL17, RpL35, mRpL11, mRpS35

    

Neural-specific measurements: high-stability mRNAs

GO term

Definition

P value

FDR

Count

Fold enrichment

0048812

Neuron projection morphogenesis

5 × 10−6

6 × 10−4

33

2.4

 

trc, fusl, Fas2, Appl, Fmr1, otk, ben

    

0003924

GTPase activity

2 × 10−4

.02

17

2.9

 

Rab23, Rab30, Rab11, Rho1, Ras64B

    

0012501

Programmed cell death

2 × 10−3

.06

17

2.4

 

grim, pten, scyl, egr, mod(mdg4)

    

0004672

Protein kinase activity

9 × 10−3

.24

23

1.8

 

CamKI, Cdk4, Ror, ald, aur, nmo, trbl

    

0019226

Transmission of nerve impulse

.02

.25

17

1.8

 

CASK, CanB, Dap160, cpx, Sap47

    

0051674

Localization of cell

.01

.16

18

1.9

 

cbl, APC, cortactin, par-6, baz, spri

    
  1. Gene ontology categories enriched among the 500 most stable and 500 least stable transcripts were identified using DAVID. Representative genes are listed for each category. FDR is the Benjamini-Hochberg false discovery rate.