Thaps_bicluster_0042 Residual: 0.43
Thalassiosira pseudonana

Module Page Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.
Title Residual Model version Organism
Thaps_bicluster_0042 0.43 Thalassiosira pseudonana
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Displaying 1 - 39 of 39
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10146 Fra10Ac1 superfamily

10146 - Fra10Ac1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

10146
10433 hypothetical protein

10433 - hypothetical protein

GO Terms:

GO:0003910

CD Domains:

Go To Gene Page:

10433
10453 hypothetical protein

10453 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10453
10497 hypothetical protein

10497 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10497
16075 tpt

16075 - tpt

GO Terms:

NA

CD Domains:

Go To Gene Page:

16075
16384 SIR2 superfamily

16384 - SIR2 superfamily

GO Terms:

GO:0003677, GO:0005677, GO:0006342, GO:0006355, GO:0004407, GO:0008418, GO:0008759, GO:0009017, GO:0016811, GO:0017159, GO:0018748, GO:0018749, GO:0047419

CD Domains:

Go To Gene Page:

16384
16675 TatD_DNAse

16675 - TatD_DNAse

GO Terms:

GO:0016888

CD Domains:

Go To Gene Page:

16675
16777 Abhydrolase_5

16777 - Abhydrolase_5

GO Terms:

GO:0003824

CD Domains:

Go To Gene Page:

16777
204 ATPase-IIA1_Ca

204 - ATPase-IIA1_Ca

GO Terms:

GO:0005524, GO:0006812, GO:0015662, GO:0016020, GO:0005388, GO:0006816, GO:0016021, GO:0003824, GO:0008152, GO:0016820

CD Domains:

Go To Gene Page:

204
2060 hypothetical protein

2060 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2060
23143 hypothetical protein

23143 - hypothetical protein

GO Terms:

GO:0000074, GO:0005634

CD Domains:

Go To Gene Page:

23143
2353 hypothetical protein

2353 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2353
24309 hypothetical protein

24309 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24309
24385 hypothetical protein

24385 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24385
260812 LPLAT_AGPAT-like

260812 - LPLAT_AGPAT-like

GO Terms:

GO:0008152, GO:0008415, GO:0003841

CD Domains:

Go To Gene Page:

260812
261278 GRX_GRXh_1_2_like

261278 - GRX_GRXh_1_2_like

GO Terms:

GO:0005489, GO:0006118, GO:0045454

CD Domains:

Go To Gene Page:

261278
261287 eIF1_SUI1

261287 - eIF1_SUI1

GO Terms:

GO:0003743, GO:0006413

CD Domains:

Go To Gene Page:

261287
263313 Peptidase_M8 superfamily

263313 - Peptidase_M8 superfamily

GO Terms:

GO:0004222, GO:0006508, GO:0007155, GO:0016020

CD Domains:

Go To Gene Page:

263313
263505 CHD

263505 - CHD

GO Terms:

GO:0007242, GO:0009190, GO:0016849, GO:0004016, GO:0008294

CD Domains:

Go To Gene Page:

263505
263799 DUF521

263799 - DUF521

GO Terms:

NA

CD Domains:

Go To Gene Page:

263799
268024 hypothetical protein

268024 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268024
270013 DNA_pol_A_plastid_like
31064 PTZ00044

31064 - PTZ00044

GO Terms:

GO:0006464

CD Domains:

Go To Gene Page:

31064
31635 tpt

31635 - tpt

GO Terms:

NA

CD Domains:

Go To Gene Page:

31635
32093 FKBP_C

32093 - FKBP_C

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

32093
33330 DPM1_like

33330 - DPM1_like

GO Terms:

GO:0004582

CD Domains:

Go To Gene Page:

33330
3541 hypothetical protein

3541 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3541
39864 DEXDc superfamily

39864 - DEXDc superfamily

GO Terms:

GO:0003676, GO:0005524, GO:0008026, GO:0004386, GO:0000810, GO:0004787, GO:0008722, GO:0008758, GO:0008796, GO:0008828, GO:0016462, GO:0016818, GO:0019176, GO:0019177

CD Domains:

Go To Gene Page:

39864
41530 Cytochrom_C superfamily

41530 - Cytochrom_C superfamily

GO Terms:

GO:0005489, GO:0006118

CD Domains:

Go To Gene Page:

41530
4402 Rotamase

4402 - Rotamase

GO Terms:

GO:0016853, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

4402
4709 Adenylation_mRNA_capping

4709 - Adenylation_mRNA_capping

GO Terms:

GO:0004484, GO:0006370, GO:0006397

CD Domains:

Go To Gene Page:

4709
6375 hypothetical protein

6375 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6375
7141 DEP

7141 - DEP

GO Terms:

GO:0007242

CD Domains:

Go To Gene Page:

7141
7940 hypothetical protein

7940 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7940
8537 S2P-M50_like_2

8537 - S2P-M50_like_2

GO Terms:

GO:0006508, GO:0008237, GO:0008270, GO:0004222

CD Domains:

Go To Gene Page:

8537
908 hypothetical protein

908 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

908
9524 hypothetical protein

9524 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9524
GO ID Go Term p-value q-value Cluster
GO:0006270 DNA replication initiation 0.0438152 1 Thaps_bicluster_0042
GO:0006355 regulation of transcription, DNA-dependent 0.793535 1 Thaps_bicluster_0042
GO:0006342 chromatin silencing 0.0438152 1 Thaps_bicluster_0042
GO:0045454 cell redox homeostasis 0.0438152 1 Thaps_bicluster_0042
GO:0009190 cyclic nucleotide biosynthesis 0.103869 1 Thaps_bicluster_0042
GO:0006397 mRNA processing 0.103869 1 Thaps_bicluster_0042
GO:0006413 translational initiation 0.112781 1 Thaps_bicluster_0042
GO:0007155 cell adhesion 0.139011 1 Thaps_bicluster_0042
GO:0006260 DNA replication 0.160299 1 Thaps_bicluster_0042
GO:0006812 cation transport 0.193316 1 Thaps_bicluster_0042
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