Thaps_bicluster_0234 Residual: 0.27
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_0234 0.27 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 17 of 17
" class="views-fluidgrid-wrapper clear-block">
1835 hypothetical protein

1835 - hypothetical protein

GO Terms:

GO:0005351, GO:0009401

CD Domains:

Go To Gene Page:

1835
20879 (Tp_CCCH21) regulator [Rayko]

20879 - (Tp_CCCH21) regulator [Rayko]

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

20879
21698 hypothetical protein

21698 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21698
22599 hypothetical protein

22599 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22599
23306 hypothetical protein

23306 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23306
23679 Diphthamide_syn superfamily

23679 - Diphthamide_syn superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23679
24123 fumC

24123 - fumC

GO Terms:

GO:0003824, GO:0004333, GO:0006106, GO:0045239

CD Domains:

Go To Gene Page:

24123
25799 TYW3 superfamily

25799 - TYW3 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

25799
263350 (RPC25) RPB7

263350 - (RPC25) RPB7

GO Terms:

GO:0003899, GO:0006350, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

263350
263872 PRK14329

263872 - PRK14329

GO Terms:

GO:0005554, GO:0003824, GO:0005506

CD Domains:

Go To Gene Page:

263872
268136 COG1054

268136 - COG1054

GO Terms:

NA

CD Domains:

Go To Gene Page:

268136
268812 HrpA

268812 - HrpA

GO Terms:

GO:0005524, GO:0008026, GO:0003676, GO:0004386

CD Domains:

Go To Gene Page:

268812
33985 PseudoU_synth_PUS1_PUS2

33985 - PseudoU_synth_PUS1_PUS2

GO Terms:

GO:0004730, GO:0008033, GO:0009982, GO:0016439

CD Domains:

Go To Gene Page:

33985
36845 (RPA2_1) RpoB

36845 - (RPA2_1) RpoB

GO Terms:

GO:0003677, GO:0003899, GO:0006350, GO:0005634, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

36845
3944 COG0218

3944 - COG0218

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

3944
39812 Sun

39812 - Sun

GO Terms:

NA

CD Domains:

Go To Gene Page:

39812
5540 hypothetical protein

5540 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5540
GO ID Go Term p-value q-value Cluster
GO:0006350 transcription 0.000367637 1 Thaps_bicluster_0234
GO:0006106 fumarate metabolism 0.0010337 1 Thaps_bicluster_0234
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0184762 1 Thaps_bicluster_0234
GO:0008033 tRNA processing 0.0184762 1 Thaps_bicluster_0234
Log in to post comments