Thaps_bicluster_0131 Residual: 0.35
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_0131 0.35 Thalassiosira pseudonana
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Displaying 1 - 24 of 24
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10892 hypothetical protein

10892 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10892
22171 hypothetical protein

22171 - hypothetical protein

GO Terms:

GO:0006812, GO:0008324, GO:0016020

CD Domains:

Go To Gene Page:

22171
2233 (atpC_1) V_ATP_synt_C

2233 - (atpC_1) V_ATP_synt_C

GO Terms:

GO:0015986, GO:0016021, GO:0016469, GO:0046933, GO:0046961, GO:0016020, GO:0003936

CD Domains:

Go To Gene Page:

2233
22820 Choline_transpo

22820 - Choline_transpo

GO Terms:

NA

CD Domains:

Go To Gene Page:

22820
23399 PTZ00184

23399 - PTZ00184

GO Terms:

GO:0005509, GO:0001539, GO:0009288

CD Domains:

Go To Gene Page:

23399
25022 AFD_class_I superfamily

25022 - AFD_class_I superfamily

GO Terms:

GO:0003824, GO:0008152, GO:0004467

CD Domains:

Go To Gene Page:

25022
25042 AFD_class_I superfamily

25042 - AFD_class_I superfamily

GO Terms:

GO:0003824, GO:0008152, GO:0004467

CD Domains:

Go To Gene Page:

25042
25789 hypothetical protein

25789 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25789
25837 hypothetical protein

25837 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25837
2648 hypothetical protein

2648 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2648
2669 MmsB

2669 - MmsB

GO Terms:

GO:0006573, GO:0008442, GO:0004616, GO:0006098

CD Domains:

Go To Gene Page:

2669
29244 cyclophilin_ABH_like

29244 - cyclophilin_ABH_like

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

29244
31535 cyclophilin_ABH_like

31535 - cyclophilin_ABH_like

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

31535
31705 Mpv17_PMP22

31705 - Mpv17_PMP22

GO Terms:

GO:0016021

CD Domains:

Go To Gene Page:

31705
32760 PDEase_I

32760 - PDEase_I

GO Terms:

GO:0004114, GO:0007165, GO:0003824, GO:0051342

CD Domains:

Go To Gene Page:

32760
3564 hypothetical protein

3564 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3564
37443 Cupin_2 superfamily

37443 - Cupin_2 superfamily

GO Terms:

GO:0016701, GO:0018553, GO:0018554

CD Domains:

Go To Gene Page:

37443
37834 ATP-synt_C superfamily

37834 - ATP-synt_C superfamily

GO Terms:

GO:0015986, GO:0016021, GO:0016469, GO:0046933, GO:0046961, GO:0016020, GO:0003936

CD Domains:

Go To Gene Page:

37834
39173 ATP-synt_D

39173 - ATP-synt_D

GO Terms:

GO:0015986, GO:0016469, GO:0046933, GO:0046961, GO:0003936

CD Domains:

Go To Gene Page:

39173
39278 ATP-synt_C

39278 - ATP-synt_C

GO Terms:

GO:0015986, GO:0016021, GO:0016469, GO:0046933, GO:0046961, GO:0016020, GO:0003936

CD Domains:

Go To Gene Page:

39278
39417 (VAT4) V_ATP_synt_C

39417 - (VAT4) V_ATP_synt_C

GO Terms:

GO:0015986, GO:0016021, GO:0016469, GO:0046933, GO:0046961, GO:0016020, GO:0003936

CD Domains:

Go To Gene Page:

39417
41697 TRX_family

41697 - TRX_family

GO Terms:

GO:0005489, GO:0006118, GO:0004791

CD Domains:

Go To Gene Page:

41697
8031 DUF1028 superfamily

8031 - DUF1028 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

8031
997 PLN02342

997 - PLN02342

GO Terms:

GO:0004070, GO:0006207, GO:0004585, GO:0006520, GO:0009348, GO:0016597, GO:0016743

CD Domains:

Go To Gene Page:

997
GO ID Go Term p-value q-value Cluster
GO:0015986 ATP synthesis coupled proton transport 0.000000655 0.00181161 Thaps_bicluster_0131
GO:0006573 valine metabolism 0.0156247 1 Thaps_bicluster_0131
GO:0001539 ciliary or flagellar motility 0.0156247 1 Thaps_bicluster_0131
GO:0051342 regulation of cyclic nucleotide phosphodiesterase activity 0.0194946 1 Thaps_bicluster_0131
GO:0006207 'de novo' pyrimidine base biosynthesis 0.0194946 1 Thaps_bicluster_0131
GO:0006098 pentose-phosphate shunt 0.02335 1 Thaps_bicluster_0131
GO:0006520 amino acid metabolism 0.0794862 1 Thaps_bicluster_0131
GO:0006457 protein folding 0.0910477 1 Thaps_bicluster_0131
GO:0006350 transcription 0.111686 1 Thaps_bicluster_0131
GO:0007165 signal transduction 0.146211 1 Thaps_bicluster_0131
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