Thaps_bicluster_0226 Residual: 0.29
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_0226 0.29 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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20737 Sun

20737 - Sun

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

20737
2157 D123 superfamily

2157 - D123 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

2157
21973 G-patch

21973 - G-patch

GO Terms:

GO:0003676, GO:0005622

CD Domains:

Go To Gene Page:

21973
22861 hypothetical protein

22861 - hypothetical protein

GO Terms:

GO:0004003, GO:0004004, GO:0008026, GO:0008094, GO:0008186, GO:0015462, GO:0015616, GO:0016887, GO:0017116, GO:0042623, GO:0042624, GO:0042625, GO:0042626

CD Domains:

Go To Gene Page:

22861
22999 hypothetical protein

22999 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22999
23209 hypothetical protein

23209 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23209
24439 hypothetical protein

24439 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24439
24907 Sas10
25183 hypothetical protein

25183 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25183
262325 SpoU_methylase

262325 - SpoU_methylase

GO Terms:

GO:0003723, GO:0006396, GO:0008173, GO:0009020

CD Domains:

Go To Gene Page:

262325
268880 WD40 superfamily

268880 - WD40 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

268880
268970 PGDH_like_3

268970 - PGDH_like_3

GO Terms:

GO:0006564, GO:0016616, GO:0004617

CD Domains:

Go To Gene Page:

268970
269975 (Tp_TAZ2) regulator [Rayko]

269975 - (Tp_TAZ2) regulator [Rayko]

GO Terms:

GO:0003712, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

269975
3018 AAT_I

3018 - AAT_I

GO Terms:

GO:0009058, GO:0004648

CD Domains:

Go To Gene Page:

3018
32790 RRM_eIF3G_like

32790 - RRM_eIF3G_like

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

32790
5104 hypothetical protein

5104 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5104
6020 DUF2088 superfamily

6020 - DUF2088 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

6020
9118 MoaC_PE

9118 - MoaC_PE

GO Terms:

GO:0006777

CD Domains:

Go To Gene Page:

9118
GO ID Go Term p-value q-value Cluster
GO:0000154 rRNA modification 0.00289256 1 Thaps_bicluster_0226
GO:0006777 Mo-molybdopterin cofactor biosynthesis 0.00865617 1 Thaps_bicluster_0226
GO:0006364 rRNA processing 0.0115273 1 Thaps_bicluster_0226
GO:0006564 L-serine biosynthesis 0.0129601 1 Thaps_bicluster_0226
GO:0009058 biosynthesis 0.0769767 1 Thaps_bicluster_0226
GO:0006396 RNA processing 0.081025 1 Thaps_bicluster_0226
GO:0006355 regulation of transcription, DNA-dependent 0.368277 1 Thaps_bicluster_0226
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