Thaps_bicluster_0246 Residual: 0.41
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_0246 0.41 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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10157 hypothetical protein

10157 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10157
10366 hypothetical protein

10366 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10366
1217 (Tp_Myb1R2) SANT_TRF

1217 - (Tp_Myb1R2) SANT_TRF

GO Terms:

GO:0003677, GO:0005634

CD Domains:

Go To Gene Page:

1217
1247 (CYS3) CBS_like

1247 - (CYS3) CBS_like

GO Terms:

GO:0003824, GO:0008152, GO:0004124

CD Domains:

Go To Gene Page:

1247
1820 SET

1820 - SET

GO Terms:

NA

CD Domains:

Go To Gene Page:

1820
1981 hypothetical protein

1981 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1981
20880 PhoD

20880 - PhoD

GO Terms:

NA

CD Domains:

Go To Gene Page:

20880
21779 hypothetical protein

21779 - hypothetical protein

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

21779
21815 (AMS1) PLN02243

21815 - (AMS1) PLN02243

GO Terms:

GO:0004478, GO:0005524, GO:0006730, GO:0048269, GO:0048270

CD Domains:

Go To Gene Page:

21815
22667 hypothetical protein

22667 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22667
23036 hypothetical protein

23036 - hypothetical protein

GO Terms:

GO:0005261, GO:0006812, GO:0016020, GO:0004866

CD Domains:

Go To Gene Page:

23036
23496 plant_peroxidase_like

23496 - plant_peroxidase_like

GO Terms:

GO:0004601, GO:0006979

CD Domains:

Go To Gene Page:

23496
23675 hypothetical protein

23675 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23675
25805 hypothetical protein

25805 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25805
263579 2A0109

263579 - 2A0109

GO Terms:

GO:0005215, GO:0006810, GO:0016021

CD Domains:

Go To Gene Page:

263579
269320 (DGD2) UGD_SDR_e

269320 - (DGD2) UGD_SDR_e

GO Terms:

GO:0003824, GO:0009225, GO:0005975, GO:0016857, GO:0008460

CD Domains:

Go To Gene Page:

269320
269889 hypothetical protein

269889 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269889
31912 (PPI1) cyclophilin_ABH_like

31912 - (PPI1) cyclophilin_ABH_like

GO Terms:

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

CD Domains:

Go To Gene Page:

31912
32964 PLN00090

32964 - PLN00090

GO Terms:

GO:0009523, GO:0016021, GO:0019684

CD Domains:

Go To Gene Page:

32964
33353 TRX_family

33353 - TRX_family

GO Terms:

GO:0005489, GO:0006118, GO:0004791

CD Domains:

Go To Gene Page:

33353
33772 S_TKc

33772 - S_TKc

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004674

CD Domains:

Go To Gene Page:

33772
38964 Chorismate_synthase

38964 - Chorismate_synthase

GO Terms:

GO:0004107, GO:0009073

CD Domains:

Go To Gene Page:

38964
644 (AK2) PTZ00247

644 - (AK2) PTZ00247

GO Terms:

GO:0004001, GO:0006166

CD Domains:

Go To Gene Page:

644
6816 GST_C_family superfamily

6816 - GST_C_family superfamily

GO Terms:

GO:0005489, GO:0006118, GO:0045454, GO:0050220

CD Domains:

Go To Gene Page:

6816
780 Glf

780 - Glf

GO Terms:

GO:0008767, GO:0009103

CD Domains:

Go To Gene Page:

780
GO ID Go Term p-value q-value Cluster
GO:0009103 lipopolysaccharide biosynthesis 0.00351458 1 Thaps_bicluster_0246
GO:0006166 purine ribonucleoside salvage 0.00351458 1 Thaps_bicluster_0246
GO:0019684 photosynthesis, light reaction 0.017457 1 Thaps_bicluster_0246
GO:0009073 aromatic amino acid family biosynthesis 0.0243591 1 Thaps_bicluster_0246
GO:0006730 one-carbon compound metabolism 0.0243591 1 Thaps_bicluster_0246
GO:0045454 cell redox homeostasis 0.0312156 1 Thaps_bicluster_0246
GO:0009225 nucleotide-sugar metabolism 0.0312156 1 Thaps_bicluster_0246
GO:0006508 proteolysis 0.0481589 1 Thaps_bicluster_0246
GO:0006979 response to oxidative stress 0.0812124 1 Thaps_bicluster_0246
GO:0006812 cation transport 0.141059 1 Thaps_bicluster_0246
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