Thaps_bicluster_0190 Residual: 0.26
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_0190 0.26 Thalassiosira pseudonana
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Displaying 1 - 15 of 15
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10273 zf-met2

10273 - zf-met2

GO Terms:

NA

CD Domains:

Go To Gene Page:

10273
1374 RRM

1374 - RRM

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

1374
21245 MPP_superfamily superfamily

21245 - MPP_superfamily superfamily

GO Terms:

GO:0016787

CD Domains:

Go To Gene Page:

21245
21933 RNA_pol_I_A49 superfamily

21933 - RNA_pol_I_A49 superfamily

GO Terms:

GO:0003993

CD Domains:

Go To Gene Page:

21933
25277 hypothetical protein

25277 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25277
260923 BcrAD_BadFG superfamily

260923 - BcrAD_BadFG superfamily

GO Terms:

GO:0003824, GO:0009058

CD Domains:

Go To Gene Page:

260923
26678 (TKT1) PLN02790

26678 - (TKT1) PLN02790

GO Terms:

GO:0004802

CD Domains:

Go To Gene Page:

26678
268745 hypothetical protein

268745 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268745
269966 (VTS1) PTZ00419

269966 - (VTS1) PTZ00419

GO Terms:

GO:0004812, GO:0005524, GO:0006418, GO:0003779, GO:0004832, GO:0006438

CD Domains:

Go To Gene Page:

269966
27083 eIF3_N superfamily

27083 - eIF3_N superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

27083
30301 PLN03206

30301 - PLN03206

GO Terms:

GO:0003824, GO:0004642, GO:0006189

CD Domains:

Go To Gene Page:

30301
31516 SIK1

31516 - SIK1

GO Terms:

NA

CD Domains:

Go To Gene Page:

31516
33871 MPP_PP5_C

33871 - MPP_PP5_C

GO Terms:

GO:0016787, GO:0000158, GO:0004721, GO:0004723, GO:0004724, GO:0005963, GO:0008420, GO:0008597, GO:0015071, GO:0017018, GO:0017020, GO:0017023, GO:0030357

CD Domains:

Go To Gene Page:

33871
37071 TIM_phosphate_binding superfamily

37071 - TIM_phosphate_binding superfamily

GO Terms:

GO:0009116, GO:0016740, GO:0004588, GO:0006221

CD Domains:

Go To Gene Page:

37071
39845 (DNA_TopoIV) PRK05560

39845 - (DNA_TopoIV) PRK05560

GO Terms:

GO:0003677, GO:0003918, GO:0005524, GO:0006259, GO:0006265, GO:0005694, GO:0006268, GO:0003916

CD Domains:

Go To Gene Page:

39845
GO ID Go Term p-value q-value Cluster
GO:0006438 valyl-tRNA aminoacylation 0.00371824 1 Thaps_bicluster_0190
GO:0006221 pyrimidine nucleotide biosynthesis 0.00557274 1 Thaps_bicluster_0190
GO:0006268 DNA unwinding 0.00927255 1 Thaps_bicluster_0190
GO:0006189 'de novo' IMP biosynthesis 0.00927255 1 Thaps_bicluster_0190
GO:0009116 nucleoside metabolism 0.0111179 1 Thaps_bicluster_0190
GO:0006265 DNA topological change 0.0184686 1 Thaps_bicluster_0190
GO:0006259 DNA metabolism 0.0257707 1 Thaps_bicluster_0190
GO:0009058 biosynthesis 0.0978804 1 Thaps_bicluster_0190
GO:0006418 tRNA aminoacylation for protein translation 0.101273 1 Thaps_bicluster_0190
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