Thaps_bicluster_0270 Residual: 0.28
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_0270 0.28 Thalassiosira pseudonana
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Displaying 1 - 15 of 15
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17110 rbgA

17110 - rbgA

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

17110
20580 hypothetical protein

20580 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20580
20626 hypothetical protein

20626 - hypothetical protein

GO Terms:

GO:0003677, GO:0003711, GO:0006355

CD Domains:

Go To Gene Page:

20626
20629 YCII superfamily

20629 - YCII superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

20629
22221 hypothetical protein

22221 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22221
23385 hypothetical protein

23385 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23385
268238 PRK05192

268238 - PRK05192

GO Terms:

GO:0006118, GO:0015036, GO:0005554

CD Domains:

Go To Gene Page:

268238
268350 SpoU_methylase

268350 - SpoU_methylase

GO Terms:

GO:0003723, GO:0006396, GO:0008173

CD Domains:

Go To Gene Page:

268350
2920 PRK05764

2920 - PRK05764

GO Terms:

GO:0009058, GO:0016847, GO:0003824, GO:0016769, GO:0004069

CD Domains:

Go To Gene Page:

2920
30691 AdoMet_MTases

30691 - AdoMet_MTases

GO Terms:

GO:0008757, GO:0003824, GO:0004766

CD Domains:

Go To Gene Page:

30691
35224 Aldo_ket_red

35224 - Aldo_ket_red

GO Terms:

GO:0016491

CD Domains:

Go To Gene Page:

35224
36186 iojap_ybeB

36186 - iojap_ybeB

GO Terms:

GO:0003910, GO:0005524, GO:0006260, GO:0006281, GO:0006310, GO:0005554

CD Domains:

Go To Gene Page:

36186
40223 PLN02347

40223 - PLN02347

GO Terms:

GO:0003824, GO:0003922, GO:0005524, GO:0006164, GO:0006177, GO:0009058

CD Domains:

Go To Gene Page:

40223
6780 hypothetical protein

6780 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6780
GO ID Go Term p-value q-value Cluster
GO:0000154 rRNA modification 0.00454357 1 Thaps_bicluster_0270
GO:0006177 GMP biosynthesis 0.00454357 1 Thaps_bicluster_0270
GO:0009058 biosynthesis 0.00653848 1 Thaps_bicluster_0270
GO:0006164 purine nucleotide biosynthesis 0.00906837 1 Thaps_bicluster_0270
GO:0006310 DNA recombination 0.0424129 1 Thaps_bicluster_0270
GO:0006260 DNA replication 0.0768533 1 Thaps_bicluster_0270
GO:0006281 DNA repair 0.0998737 1 Thaps_bicluster_0270
GO:0006396 RNA processing 0.124391 1 Thaps_bicluster_0270
GO:0006118 electron transport 0.463588 1 Thaps_bicluster_0270
GO:0006355 regulation of transcription, DNA-dependent 0.514255 1 Thaps_bicluster_0270
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