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Biology Articles » Methods & Techniques » Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system » Tables

Tables
- Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system

Table 1
Expression of promoter-GFP reporters for transcripts enriched in the embryonic pan-neural, larval pan-neural or A-class motor neuron datasets



Pan-neural
 A-class



Cosmid
 Gene
 Protein
 EP fold change
 LP fold change
 In neurons*
 Fold change
 UNC-4 neuron(s)*
C01G6.4
Predicted E3 ubiquitin ligase
 1.8
 -
 √
 -
 VA, DA
VF11C1L.1
 ppk-3
 PIP kinase
 1.8
 -
 √
 -
 VA, DA
C25D7.8
Novel
 1.9
 -
 √
 -
 VA, DA
F08G12.1

3.0
 -
 √
 -
 VA, DA
M79.1
 abl-1
 Abelson kinase
 2.3
 -
 √
 -
 VA, DA
F25G6.4
 acr-15
 Acetylcholine receptor
 -
 4.9
 √
 -
 VA, DA
T27A1.6
 mab-9
 Transcription factor
 -
 1.7
 √
 -
 DA
F39G3.8
 tig-2
 TGF-β
 -
 1.8
 √
 -
 VA, DA
T19C4.5
Novel
 -
 2.0
-
CC4.2
 nlp-15
 Neuropeptide
 -
 6.5
 √
 -
C18H9.7
 rpy-1
 Rapsyn
 -
 2.7
 √
 -
 DA
Y71D11A.5
Ligand-gated ion channel
 2.1
 1.8
 √
 -
C04E12.7
Phospholipid scramblase
 -
 3.2
 √
 1.8
 VA, DA
F36A2.4
 twk-30
 K+ channel
 -
 2.1
 √
 5.1
 VA, DA
Y71H9A.3
 sto-4
 Stomatin
 -
 3.0
 √
 1.6
 VA
F29G6.2
Novel
 -
 3.2
 √
 1.6
 VA, DA,SAB, I5, AVF
C44B11.3
 mec-12
 Alpha-tubulin
 -
 5.9
 √
 1.9
 VA, DA
T23D8.2
 tsp-7
 Tetraspanin
 -
 3.5
 √
 4.8
 VA, DA
T05C12.2
 acr-14
 Acetylcholine receptor
 -
 1.5
 √
 3.1
 DA
F33D4.3
 flp-13
 Neuropeptide
 -
 7.1
 √
 7.9
 I5
C11D2.6
 nca-1
 Ca++ channel
 -
 2.3
 √
 2.2
 VA, DA
E03D2.2
 nlp-9
 Neuropeptide
 -
 3.1
 √
 2.5
 VA
F55C12.4
Novel
 -
 3.5
 √
 2.1
 DA
F43C9.4
 mig-13
 CUB domain
 -
 1.8
 √
 2.8
 VA, DA
F39B2.8
Predicted membrane protein
 1.7
 3.5
 √
 2.1
 VA, DA
K02E10.8
 syg-1
 Ig domain
 1.8
 1.8
 √
 1.8
 VA, DA
ZC21.2
 trp-1
 Ca++ channel
 1.9
 2.2
 √
 1.9
 VA, DA
Y47D3B.2a
 nlp-21
 Neuropeptide
 3.9
 8.3
 √
 3.7
 VA, DA
F09C3.2
Phosphatase
 1.9
 2.7
 √
 1.7
 VA, DA
T27E9.9
Ligand-gated ion channel
 2.3
 4.0
 √
 3.1
Y34D9B.1
 mig-1
 Frizzled-like
 -
 -
 √
 1.6
 VA, DA
*GFP expression in neurons (check mark), and in A-class motor neurons (DA, VA, SAB, I5). GFP expression was typically determined in L2 larvae. Full expression patterns can be found in Additional data file 17. Expression patterns for some of these GFP reporters have been previously reported: T27A1.6, F39G3.8, T19C4.5, CC4.2, C18H9.7, F36A2.4, F29G6.2, T23D8.2, T05C12.2, F33D4.3, C11D2.6, E03D2.2, F55C12.4, F43C9.4, K02E10.8, ZC21.2, Y47D3B.2a, F09C3.2 [5]; F33D4.3 [43]; CC4.2, E03D2.2 [96]; F36A2.4, [121]; F43C9.4, [122]. Y47D3B.2a, [123].
Table 2
Transcripts enriched in C. elegans neurons
Category
 Embryonic pan-neural
 Larval pan-neural
 Embryonic A-class
 Larval A-class
Ion channels/receptors/membrane proteins
 122
 156
 60
 41
      Acetylcholine receptors
13
 24
 9
 9
      GABA receptors
1
 4
3
      Glutamate receptors
8
 8
 1
 2
      Potassium channels
11
 24
 8
 10
      Calcium channels
8
 10
 7
 4
      DEG/ENaC channels
3
 10
 1
 1
      Stomatins
3
 7
 2
 1
      Other ligand-gated ion channels
6
 13
 2
 2
      Gap junction proteins (innexins)
4
 4
 1
 1
      Symporters/exchangers/transporters
24
 27
 12
 3
      Other membrane proteins
41
 25
 17
 5





Axon guidance
 4
 8
 8
 3





Adhesion/Ig domain
 6
 17
 10
 11





Cytoskeleton-related
 33
 34
 16
 5





Transcriptional control
 90
 91
 38
 10
      Homeobox
8
 28
 3
 3
      Hormone receptors
24
 15
 5
 1
      Aryl-hydrocarbon receptors
1
 3
 1
      SMADs

3
 1
 1
      HMG box
5
 5

      HLH factors
2
 4
 1
 1
      Other transcription factors
32
 25
 13
 4
      General factors
18
 8
 14





Kinase/phosphatase
 82
 79
 51
 18





GPCR signaling
 107
 169
 42
 25
      G-protein coupled receptors
85
 137
 33
 18
      G-proteins
8
 10
 3
 3
      Regulators of G-protein signaling (GTPases, GEFs, GRKs)
7
 8
 4
 2
      Adenylate/guanylate cyclases
7
 14
 2
 2





Rab/Rho/Rac GTPase signaling
 17
 7
 7
 2





Neuropeptides
 39
 58
 11
 13
      FMRFamide-like (flp)
13
 20
 4
 5
      Neuropeptide-like (nlp)
13
 18
 3
 4
      Insulin-like
9
 11
 2
 1
      TGF-beta
1
 3
 1
 1
      Pro-protein convertases
3
 6
 1
 3





Calcium binding
 18
 26
 12
 9





Synaptic vesicle associated
 38
 53
 25
 17





RNA binding
 22
 14
 22
 3





Ubiquitin associated
 39
 19
 12
 3





Enzymes
 199
 103
 111
 30





Collagens
 2
 1
 5
 24





Other
 297
 205
 174
 44





Unnamed/uncharacterized
 159
 127
 161
 56





Unclassified
 363
 395
 230
 98





Total
 1,637
 1,562
 995
 412
Table 3
Major transcription factor families enriched in C. elegans neurons
Transcription factor families
 Fold change
Cosmid name
 Common name
 Embryonic pan-neural
 Larval pan-neural
 Embryonic A-class
 Larval A-class
Homeobox




      C40H5.5
ttx-3
 1.6
 1.5

      C33D12.1
ceh-31
1.6

      D1007.1
ceh-17
1.6

      K02B12.1
ceh-6
1.6
1.6
      T13C5.4

3.3
 1.6

      T26C11.7
ceh-39
1.6

      ZC64.3
ceh-18
1.6

      C18B12.3


1.7

      C28A5.4
ceh-43
1.7

      F56A12.1
unc-39
1.8

      W03A3.1
ceh-10
1.8

      C10G8.6
ceh-34
1.9

      C17H12.9


2

      F55B12.1
ceh-24
2

      ZC123.3

1.6
 2

      C30A5.7
unc-86
2.1

      T26C11.5
ceh-41
 1.6
 2.1

      C39E6.4
mls-2
2.3

      F01D4.6
mec-3
2.6

      R08B4.2


2.6

      B0564.10
unc-30
 2.2
 2.7

      W05E10.3
ceh-32
2.7

      F26C11.2
unc-4
2.8
 13.2
 9.0
      C37E2.4
ceh-36
2.9

      R07B1.1
vab-15
2.9

      Y54F10AM.4
ceh-44
3.3
2.1
      F58E6.10
unc-42
 2.4
 3.8

      ZC247.3
lin-11
5.2

      C07E3.5

1.7


      F46C8.5
ceh-14
 1.7


      W06A7.3
ret-1

1.8
      Y113G7A.6
ttx-1

2.8






Hormone receptors




      Y94H6A.1


1.5

      F47C10.3


1.6

      F47C10.7


1.6

      F56E3.4
fax-1
1.7

      H01A20.1
nhr-3
 1.8
 1.7
 1.9
      R09G11.2
nhr-1
1.7

      T03G6.2
nhr-40
1.7

      Y39B6A.17
nhr-95
 1.6
 1.7
 1.8
      C24G6.4
nhr-47
 2
 1.8

      K06B4.8


2

      K06B4.1
nhr-51
 2.5
 2.1

      K06B4.2
nhr-52
2.1

      F21D12.1
nhr-21
2.2

      C49F5.4


2.9

      F07C3.10
nhr-63
4

      C06C6.4
nhr-67
 1.8


      C08F8.8
nhr-124
 1.5


      C17E7.8
nhr-116
 2.3


      F09C6.9

3.3
1.9
      F16B4.9

1.9


      F31F4.12

1.6


      F41B5.9
nhr-96
 2.5
1.7
      F44C8.11

1.8


      F44C8.9

1.7


      F48G7.11

2


      F59E11.8

1.8


      K06B4.10
nhr-88


1.8
      K08A2.5
nhr-71
 1.5


      K11E4.5

1.8


      R07B7.15
nhr-104
 1.7


      R11E3.5



1.8
      T07C5.4
nhr-44
 3.2


      T19A5.4
nhr-59
 1.9


      T27B7.1
nhr-115
 1.7


      T27B7.4
nhr-65
 2.9


      Y17D7A.3

1.5


      Y67D8B.2

1.8








Aryl-hydrocarbon receptors




      C25A1.11
aha-1
1.7

      C41G7.5
ahr-1
1.7

      C56C10.10

2.2
 2
 2.3






SMADs




      F01G10.8
daf-14
1.7

      F25E2.5
daf-3
1.9

      F37D6.6
tag-68
2.2
 2.3
 2.0






HMG box




      F40E10.2
sox-3
 1.6
 1.5

      T22B7.1
egl-13
1.6

      T05A7.4
hmg-11
 2.3
 2.1

      F47G4.6


2.3

      K08A8.2
sox-2
 2.5
 2.9

      C12D12.5

4.7


      Y17G7A.1
hmg-12
 1.8








HLH factors




      C43H6.8
hlh-15
 4.4
 1.6

      F58A4.7
hlh-11
1.6

      Y16B4A.1
unc-3
2.9
 3
 4.9
      F48D6.3
hlh-13
3

      W02C12.3

1.8


Table 4
Genes expressed in mechanosensory neurons are differentially detected in the larval pan-neural dataset versus the larval A-class dataset
Cosmid name
 Gene name
 Fold change
 Description





Pan-neural
 A-class
F14D12.4
 mec-2
 2.9
 -
 Prohibitins and stomatins of the PID superfamily
F01D4.6
 mec-3
 2.6
 -
 Transcription factor, contains HOX domain
T01C8.7
 mec-4
 2.7
 -
 Non voltage-gated ion channels (DEG/ENaC family)
W02D3.3
 mec-6
 1.9
 -
 Unnamed protein
ZK154.3
 mec-7
 3.6
 -
 Beta-tubulin
F16F9.5
 mec-10
 1.8
 -
 Non-voltage-gated ion channels (DEG/ENaC family)
F57H12.7
 mec-17
 7.6
 -
 Uncharacterized conserved protein
C52B9.9
 mec-18
 3.1
 -
 Acyl-CoA synthetase
C44B11.3
 mec-12
 5.9
 1.9
 Alpha-tubulin

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