Thaps_bicluster_0208 Residual: 0.25
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_0208 0.25 Thalassiosira pseudonana
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Displaying 1 - 17 of 17
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21667 (Lhcf7) fucoxanthin chlorophyll a/c light-harvesting protein, major type

21667 - (Lhcf7) fucoxanthin chlorophyll a/c light-harvesting protein, major type

GO Terms:

NA

CD Domains:

Go To Gene Page:

21667
2342 (Lhcr11) fucoxanthin chlorophyll a/c light-harvesting protein

2342 - (Lhcr11) fucoxanthin chlorophyll a/c light-harvesting protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2342
24080 (Lhcr1) fucoxanthin chl a/c light-harvesting protein, lhcr type

24080 - (Lhcr1) fucoxanthin chl a/c light-harvesting protein, lhcr type

GO Terms:

NA

CD Domains:

Go To Gene Page:

24080
25402 (Lhcf10) fucoxanthin chl a/c light-harvesting protein, major type

25402 - (Lhcf10) fucoxanthin chl a/c light-harvesting protein, major type

GO Terms:

NA

CD Domains:

Go To Gene Page:

25402
260392 (Lhcf2) fucoxanthin chlorophyll a/c protein 2

260392 - (Lhcf2) fucoxanthin chlorophyll a/c protein 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

260392
261232 URO-D

261232 - URO-D

GO Terms:

GO:0004853, GO:0006779

CD Domains:

Go To Gene Page:

261232
262032 hypothetical protein

262032 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

262032
270221 hypothetical protein

270221 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270221
270233 hypothetical protein

270233 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270233
270241 (Lhcf11) fucoxanthin-chlorophyll a-c binding protein, plastid precursor

270241 - (Lhcf11) fucoxanthin-chlorophyll a-c binding protein, plastid precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

270241
270280 hypothetical protein

270280 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270280
270316 hypothetical protein

270316 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270316
32201 Cob-chelat-sub

32201 - Cob-chelat-sub

GO Terms:

GO:0015979, GO:0015995, GO:0016851, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

32201
35871 2-Hacid_dh_1

35871 - 2-Hacid_dh_1

GO Terms:

GO:0006564, GO:0016616

CD Domains:

Go To Gene Page:

35871
37615 NADB_Rossmann superfamily

37615 - NADB_Rossmann superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

37615
4440 hypothetical protein

4440 - hypothetical protein

GO Terms:

GO:0003677

CD Domains:

Go To Gene Page:

4440
5240 ALAD_PBGS_aspartate_rich

5240 - ALAD_PBGS_aspartate_rich

GO Terms:

GO:0004655, GO:0006783

CD Domains:

Go To Gene Page:

5240
GO ID Go Term p-value q-value Cluster
GO:0015995 chlorophyll biosynthesis 0.00412967 1 Thaps_bicluster_0208
GO:0006783 heme biosynthesis 0.00412967 1 Thaps_bicluster_0208
GO:0006564 L-serine biosynthesis 0.00927255 1 Thaps_bicluster_0208
GO:0006779 porphyrin biosynthesis 0.0113237 1 Thaps_bicluster_0208
GO:0015979 photosynthesis 0.0133715 1 Thaps_bicluster_0208
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