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Table 4 The most significantly differentially represented genome features between Ribo-Zero and poly(A) transcriptomes

From: Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis

Gene ID

logFC (Ribo-Zero/poly(A))a

logCPMb

Adjusted P-valuec

Description

AFUN015353

6.73

7.69

1.31E-89

Signal recognition particle (ncRNA)

AFUN015615

7.08

5.27

2.65E-75

Signal recognition particle (ncRNA)

AFUN010049

5.05

5.25

3.80E-71

Histone H3

AFUN015157

4.18

6.81

5.86E-62

-

AFUN009381

4.64

5.73

7.90E-58

-

AFUN008241

4.17

8.62

2.49E-47

-

AFUN003688

4.43

7.35

1.91E-46

-

AFUN014500

3.78

7.48

7.14E-44

-

AFUN014369

3.71

5.84

1.51E-41

-

AFUN015010

4.84

5.04

9.84E-41

-

AFUN002493

3.46

7.32

3.88E-40

Unknown, contains cadherin domains

AFUN000145

3.49

4.93

2.31E-39

-

AFUN008247

4.98

3.75

4.38E-37

-

AFUN005891

5.19

3.75

7.85E-37

-

AFUN011958

4.05

4.83

2.41E-36

Retrotransposon, putative

AFUN011227

3.50

5.80

1.43E-35

Unknown, contains cadherin domains

AFUN008652

3.03

5.65

3.24E-34

Histone H2A

AFUN011228

3.62

5.06

3.96E-33

Unknown, contains cadherin domains

AFUN000984

2.81

6.53

2.55E-32

Unknown, contains PH-domain

AFUN002265

2.94

5.61

4.67E-32

odz/ten-m gene, putative

AFUN010223

−2.72

6.94

5.66E-26

60S ribosomal protein L39

AFUN004938

−2.45

5.25

4.22E-25

Small nuclear ribonucleoprotein D3

nad3

−4.18

8.12

1.15E-22

Nad3

AFUN005575

−2.96

4.91

1.03E-21

Estrogen receptor binding site associated antigen 9 variant 1

AFUN008128

−2.06

5.96

9.59E-19

Transcription initiation factor TFIIF subunit alpha

AFUN005032

−1.86

6.56

6.57E-18

mRNA turnover protein 4

AFUN014198

−2.51

9.41

1.94E-16

40S ribosomal protein S29

AFUN011059

−2.05

5.27

6.44E-15

-

AFUN001216

−1.94

5.18

1.12E-14

-

AFUN006762

−2.43

9.41

4.03E-14

-

AFUN009976

−1.82

6.48

9.17E-14

Nuclear protein NHN1

AFUN014520

−2.04

5.27

9.09E-13

CCR4-NOT transcription complex subunit 7/8

AFUN014691

−1.91

5.50

9.63E-13

-

AFUN002476

−3.32

6.87

2.21E-12

-

nad6

−2.65

8.06

2.44E-12

Nad6

AFUN009128

−1.69

5.29

2.86E-12

Nat13 protein

AFUN007527

−2.88

2.97

5.92E-12

Phosphopantothenoylcysteine decarboxylase

AFUN005236

−1.84

8.05

6.25E-12

40S ribosomal protein S21

AFUN003657

−1.77

5.92

6.78E-12

-

AFUN010447

−2.04

4.37

1.08E-11

26 proteasome complex subunit DSS1

  1. aLog2 fold change between ‘expression’ levels in Ribo-Zero and poly(A) samples (for values >0, Ribo-Zero > poly(A); for values <0, poly(A) > Ribo-Zero)
  2. bLog2 counts per million mapped reads. Mean ‘expression’ level for all samples
  3. cSignificance of differential ‘expression’, P-value adjusted for a 5 % false discovery rate