Thaps_bicluster_0088 Residual: 0.37
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_0088 0.37 Thalassiosira pseudonana
Displaying 1 - 29 of 29
11777 Methyltransf_16 superfamily

11777 - Methyltransf_16 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

11777
13551 Uup

13551 - Uup

GO Terms:

GO:0005524, GO:0016887, GO:0000166, GO:0017111, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

13551
13884 Uup

13884 - Uup

GO Terms:

GO:0005524, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

13884
18109 COG2119

18109 - COG2119

GO Terms:

GO:0005554, GO:0016020

CD Domains:

Go To Gene Page:

18109
25587 hypothetical protein

25587 - hypothetical protein

GO Terms:

GO:0000151, GO:0004842, GO:0008270, GO:0016567, GO:0008152, GO:0016740, GO:0003676, GO:0005634

CD Domains:

Go To Gene Page:

25587
25793 hypothetical protein

25793 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25793
261083 (Tp_sigma70.1) Sig70-cyanoRpoD

261083 - (Tp_sigma70.1) Sig70-cyanoRpoD

GO Terms:

GO:0003677, GO:0003700, GO:0006352, GO:0006355, GO:0016987

CD Domains:

Go To Gene Page:

261083
263707 Mito_carr

263707 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020

CD Domains:

Go To Gene Page:

263707
268718 (ANS1) PLN02549

268718 - (ANS1) PLN02549

GO Terms:

GO:0008152, GO:0004066, GO:0006529

CD Domains:

Go To Gene Page:

268718
269704 PRK09225

269704 - PRK09225

GO Terms:

GO:0003676, GO:0006520, GO:0003824, GO:0008152, GO:0004795, GO:0009088

CD Domains:

Go To Gene Page:

269704
269764 RluA

269764 - RluA

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0016439

CD Domains:

Go To Gene Page:

269764
27892 OAT_like

27892 - OAT_like

GO Terms:

GO:0008483, GO:0030170, GO:0004587

CD Domains:

Go To Gene Page:

27892
28100 DHBP_synthase

28100 - DHBP_synthase

GO Terms:

GO:0008686, GO:0009231

CD Domains:

Go To Gene Page:

28100
30939 S1_IF1

30939 - S1_IF1

GO Terms:

GO:0003743, GO:0006413, GO:0003723

CD Domains:

Go To Gene Page:

30939
33161 prfA

33161 - prfA

GO Terms:

GO:0003747, GO:0006415, GO:0005737, GO:0016149, GO:0004045

CD Domains:

Go To Gene Page:

33161
3438 hypothetical protein

3438 - hypothetical protein

GO Terms:

GO:0005351, GO:0009401

CD Domains:

Go To Gene Page:

3438
36576 TypA

36576 - TypA

GO Terms:

GO:0005525, GO:0006412, GO:0003924, GO:0008547

CD Domains:

Go To Gene Page:

36576
41403 ABCC_MRP_domain2

41403 - ABCC_MRP_domain2

GO Terms:

GO:0005524, GO:0006810, GO:0016021, GO:0042626, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

41403
41892 PtrB

41892 - PtrB

GO Terms:

GO:0006508, GO:0008236, GO:0004287, GO:0004252, GO:0008945

CD Domains:

Go To Gene Page:

41892
42307 GTP_HflX

42307 - GTP_HflX

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

42307
511 (GBP1) PRK09601

511 - (GBP1) PRK09601

GO Terms:

GO:0005525, GO:0005554

CD Domains:

Go To Gene Page:

511
6760 (Tp_sigma70.7) regulator [Rayko]

6760 - (Tp_sigma70.7) regulator [Rayko]

GO Terms:

GO:0003677, GO:0003700, GO:0006352, GO:0006355, GO:0016987

CD Domains:

Go To Gene Page:

6760
7310 hypothetical protein

7310 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7310
8533 hypothetical protein

8533 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8533
8808 COG0398

8808 - COG0398

GO Terms:

NA

CD Domains:

Go To Gene Page:

8808
ThpsCp028 (rpl11) ribosomal protein L11

ThpsCp028 - (rpl11) ribosomal protein L11

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp028
ThpsCp030 (rpl12) ribosomal protein L12

ThpsCp030 - (rpl12) ribosomal protein L12

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp030
ThpsCp082 (rpl34) ribosomal protein L34

ThpsCp082 - (rpl34) ribosomal protein L34

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp082
ThpsCp134 (rpl34) ribosomal protein L34

ThpsCp134 - (rpl34) ribosomal protein L34

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp134
GO ID Go Term p-value q-value Cluster
GO:0006352 transcription initiation 0.00123297 1 Thaps_bicluster_0088
GO:0006529 asparagine biosynthesis 0.00825334 1 Thaps_bicluster_0088
GO:0009088 threonine biosynthesis 0.00825334 1 Thaps_bicluster_0088
GO:0006415 translational termination 0.0245663 1 Thaps_bicluster_0088
GO:0009231 riboflavin biosynthesis 0.0245663 1 Thaps_bicluster_0088
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0719895 1 Thaps_bicluster_0088
GO:0006520 amino acid metabolism 0.0834984 1 Thaps_bicluster_0088
GO:0006413 translational initiation 0.0948716 1 Thaps_bicluster_0088
GO:0006810 transport 0.17526 1 Thaps_bicluster_0088
GO:0006396 RNA processing 0.214744 1 Thaps_bicluster_0088
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