Thaps_bicluster_0276 Residual: 0.21
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_0276 0.21 Thalassiosira pseudonana
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Displaying 1 - 18 of 18
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18198 RRM_NIFK_like

18198 - RRM_NIFK_like

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

18198
21553 Nop16 superfamily

21553 - Nop16 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21553
21725 Brix superfamily

21725 - Brix superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21725
21979 DUF2373 superfamily

21979 - DUF2373 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21979
22099 hypothetical protein

22099 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22099
22203 (Tp_CCHH28) zf-C2H2_2

22203 - (Tp_CCHH28) zf-C2H2_2

GO Terms:

GO:0003676, GO:0005634, GO:0008270

CD Domains:

Go To Gene Page:

22203
25746 hypothetical protein

25746 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25746
268003 hypothetical protein

268003 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268003
268417 hypothetical protein

268417 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268417
269776 Ribosomal_L1

269776 - Ribosomal_L1

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

269776
28755 NSA2

28755 - NSA2

GO Terms:

GO:0005622

CD Domains:

Go To Gene Page:

28755
30833 Bystin

30833 - Bystin

GO Terms:

NA

CD Domains:

Go To Gene Page:

30833
31465 Brix

31465 - Brix

GO Terms:

NA

CD Domains:

Go To Gene Page:

31465
34959 DUS_like_FMN

34959 - DUS_like_FMN

GO Terms:

GO:0008033, GO:0016491, GO:0050660, GO:0051341

CD Domains:

Go To Gene Page:

34959
36406 Ribosomal_L7_archeal_euk

36406 - Ribosomal_L7_archeal_euk

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

36406
39003 NIP7

39003 - NIP7

GO Terms:

GO:0003723

CD Domains:

Go To Gene Page:

39003
40509 (RL30) Ribosomal_L24e_L24

40509 - (RL30) Ribosomal_L24e_L24

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

40509
GO ID Go Term p-value q-value Cluster
GO:0006412 protein biosynthesis 0.000377351 1 Thaps_bicluster_0276
GO:0051341 regulation of oxidoreductase activity 0.0235597 1 Thaps_bicluster_0276
GO:0008033 tRNA processing 0.0184762 1 Thaps_bicluster_0276
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