Thaps_bicluster_0256 Residual: 0.42
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_0256 0.42 Thalassiosira pseudonana
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Displaying 1 - 32 of 32
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10731 DENR_C

10731 - DENR_C

GO Terms:

GO:0003743, GO:0006413

CD Domains:

Go To Gene Page:

10731
11731 hypothetical protein

11731 - hypothetical protein

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

11731
13482 PLN02830

13482 - PLN02830

GO Terms:

NA

CD Domains:

Go To Gene Page:

13482
16236 Nuc_sug_transp

16236 - Nuc_sug_transp

GO Terms:

GO:0005338, GO:0015780, GO:0016021, GO:0000139, GO:0005351, GO:0008643

CD Domains:

Go To Gene Page:

16236
1964 hypothetical protein

1964 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1964
21040 hypothetical protein

21040 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21040
21211 O-FucT_like

21211 - O-FucT_like

GO Terms:

NA

CD Domains:

Go To Gene Page:

21211
2122 GIY-YIG_SLX1

2122 - GIY-YIG_SLX1

GO Terms:

GO:0004518, GO:0005622, GO:0006281

CD Domains:

Go To Gene Page:

2122
21260 hypothetical protein

21260 - hypothetical protein

GO Terms:

GO:0005509, GO:0004308

CD Domains:

Go To Gene Page:

21260
21892 hypothetical protein

21892 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21892
2377 hypothetical protein

2377 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2377
24401 hypothetical protein

24401 - hypothetical protein

GO Terms:

GO:0005515, GO:0004339

CD Domains:

Go To Gene Page:

24401
24835 hypothetical protein

24835 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24835
25526 hypothetical protein

25526 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25526
25735 hypothetical protein

25735 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25735
261817 LPLAT_AGPAT-like

261817 - LPLAT_AGPAT-like

GO Terms:

GO:0008152, GO:0008415, GO:0003841, GO:0008654, GO:0016020

CD Domains:

Go To Gene Page:

261817
264314 PLN02605

264314 - PLN02605

GO Terms:

GO:0046509

CD Domains:

Go To Gene Page:

264314
268060 pepsin_retropepsin_like superfamily

268060 - pepsin_retropepsin_like superfamily

GO Terms:

GO:0004190, GO:0009049, GO:0042499, GO:0042500

CD Domains:

Go To Gene Page:

268060
269714 nt_trans superfamily

269714 - nt_trans superfamily

GO Terms:

GO:0000103, GO:0004781, GO:0005524, GO:0016301, GO:0016772, GO:0000287, GO:0008152, GO:0016462, GO:0004427, GO:0005737

CD Domains:

Go To Gene Page:

269714
31003 gpsA

31003 - gpsA

GO Terms:

GO:0005975, GO:0016614, GO:0004367, GO:0006072, GO:0009331, GO:0005737, GO:0016616, GO:0046168, GO:0051287

CD Domains:

Go To Gene Page:

31003
32507 RRF

32507 - RRF

GO Terms:

GO:0006412

CD Domains:

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32507
3318 hypothetical protein

3318 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3318
3520 hypothetical protein

3520 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3520
36481 UAA

36481 - UAA

GO Terms:

GO:0031177

CD Domains:

Go To Gene Page:

36481
4321 HAD_2

4321 - HAD_2

GO Terms:

GO:0003824, GO:0008152, GO:0008967

CD Domains:

Go To Gene Page:

4321
4433 hypothetical protein

4433 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4433
6983 hypothetical protein

6983 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6983
7138 PI-PLCc_GDPD_SF superfamily

7138 - PI-PLCc_GDPD_SF superfamily

GO Terms:

GO:0004629, GO:0007165, GO:0007242

CD Domains:

Go To Gene Page:

7138
8526 AarF

8526 - AarF

GO Terms:

NA

CD Domains:

Go To Gene Page:

8526
8748 Cnd1

8748 - Cnd1

GO Terms:

NA

CD Domains:

Go To Gene Page:

8748
9741 hypothetical protein

9741 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9741
GO ID Go Term p-value q-value Cluster
GO:0046168 glycerol-3-phosphate catabolism 0.0105089 1 Thaps_bicluster_0256
GO:0000103 sulfate assimilation 0.0139887 1 Thaps_bicluster_0256
GO:0006072 glycerol-3-phosphate metabolism 0.0139887 1 Thaps_bicluster_0256
GO:0015780 nucleotide-sugar transport 0.017457 1 Thaps_bicluster_0256
GO:0006270 DNA replication initiation 0.0312156 1 Thaps_bicluster_0256
GO:0008654 phospholipid biosynthesis 0.0481589 1 Thaps_bicluster_0256
GO:0008643 carbohydrate transport 0.0481589 1 Thaps_bicluster_0256
GO:0008152 metabolism 0.0487771 1 Thaps_bicluster_0256
GO:0006413 translational initiation 0.0812124 1 Thaps_bicluster_0256
GO:0007165 signal transduction 0.13186 1 Thaps_bicluster_0256
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