Thaps_bicluster_0184 Residual: 0.33
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_0184 0.33 Thalassiosira pseudonana
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Displaying 1 - 21 of 21
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11606 hypothetical protein

11606 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11606
1366 Abi

1366 - Abi

GO Terms:

NA

CD Domains:

Go To Gene Page:

1366
20682 hypothetical protein

20682 - hypothetical protein

GO Terms:

GO:0004553, GO:0005975

CD Domains:

Go To Gene Page:

20682
21770 PseudoU_synth_RluCD_like

21770 - PseudoU_synth_RluCD_like

GO Terms:

GO:0003723, GO:0006396, GO:0009982

CD Domains:

Go To Gene Page:

21770
21943 Gar1 superfamily

21943 - Gar1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21943
22302 Peptidase_C19 superfamily

22302 - Peptidase_C19 superfamily

GO Terms:

GO:0004197, GO:0004221, GO:0006511

CD Domains:

Go To Gene Page:

22302
22728 hypothetical protein

22728 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22728
23922 (Tp_AP2-EREBP9) regulator [Rayko]

23922 - (Tp_AP2-EREBP9) regulator [Rayko]

GO Terms:

GO:0003700, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

23922
2479 hypothetical protein

2479 - hypothetical protein

GO Terms:

GO:0015992, GO:0016020, GO:0016469, GO:0016820

CD Domains:

Go To Gene Page:

2479
26071 (PSB_1) Ntn_hydrolase superfamily

26071 - (PSB_1) Ntn_hydrolase superfamily

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

26071
262555 AAT_I superfamily

262555 - AAT_I superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

262555
262625 gatB

262625 - gatB

GO Terms:

GO:0006412, GO:0017068, GO:0016874, GO:0016884

CD Domains:

Go To Gene Page:

262625
263644 (TopoII_2) PLN03128

263644 - (TopoII_2) PLN03128

GO Terms:

GO:0003677, GO:0003918, GO:0005524, GO:0006259, GO:0006265

CD Domains:

Go To Gene Page:

263644
269449 hypothetical protein

269449 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269449
269893 TOPRIM_DnaG_primases

269893 - TOPRIM_DnaG_primases

GO Terms:

GO:0003676, GO:0006304, GO:0003896, GO:0006269

CD Domains:

Go To Gene Page:

269893
35164 acolac_lg

35164 - acolac_lg

GO Terms:

GO:0003984

CD Domains:

Go To Gene Page:

35164
35194 hypothetical protein

35194 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

35194
37928 PLN03238

37928 - PLN03238

GO Terms:

GO:0003676, GO:0005634, GO:0008270, GO:0004402

CD Domains:

Go To Gene Page:

37928
41953 RtcB

41953 - RtcB

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

41953
508 CBF5

508 - CBF5

GO Terms:

GO:0003723, GO:0004730, GO:0006396

CD Domains:

Go To Gene Page:

508
7151 hypothetical protein

7151 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7151
GO ID Go Term p-value q-value Cluster
GO:0006511 ubiquitin-dependent protein catabolism 0.0067247 1 Thaps_bicluster_0184
GO:0006304 DNA modification 0.00742571 1 Thaps_bicluster_0184
GO:0006269 DNA replication, synthesis of RNA primer 0.00742571 1 Thaps_bicluster_0184
GO:0006396 RNA processing 0.00863467 1 Thaps_bicluster_0184
GO:0006265 DNA topological change 0.0245562 1 Thaps_bicluster_0184
GO:0006259 DNA metabolism 0.034223 1 Thaps_bicluster_0184
GO:0015992 proton transport 0.0366259 1 Thaps_bicluster_0184
GO:0005975 carbohydrate metabolism 0.171169 1 Thaps_bicluster_0184
GO:0006412 protein biosynthesis 0.342653 1 Thaps_bicluster_0184
GO:0006355 regulation of transcription, DNA-dependent 0.545155 1 Thaps_bicluster_0184
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