Thaps_bicluster_0127 Residual: 0.38
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_0127 0.38 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 31 of 31
" class="views-fluidgrid-wrapper clear-block">
10378 SugarP_isomerase superfamily

10378 - SugarP_isomerase superfamily

GO Terms:

GO:0017057

CD Domains:

Go To Gene Page:

10378
1636 hypothetical protein

1636 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1636
19526 PRK07449

19526 - PRK07449

GO Terms:

NA

CD Domains:

Go To Gene Page:

19526
1973 hypothetical protein

1973 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1973
22114 hypothetical protein

22114 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22114
22711 hypothetical protein

22711 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22711
22712 hypothetical protein

22712 - hypothetical protein

GO Terms:

GO:0005489, GO:0005506, GO:0006118

CD Domains:

Go To Gene Page:

22712
23363 hypothetical protein

23363 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23363
25570 hypothetical protein

25570 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25570
25867 5_nucleotid superfamily

25867 - 5_nucleotid superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

25867
26190 SHMT

26190 - SHMT

GO Terms:

GO:0004372, GO:0006544, GO:0006563

CD Domains:

Go To Gene Page:

26190
262367 TPM

262367 - TPM

GO Terms:

NA

CD Domains:

Go To Gene Page:

262367
270328 hypothetical protein

270328 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270328
270343 hypothetical protein

270343 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270343
270373 hypothetical protein

270373 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270373
28326 lytB_ispH

28326 - lytB_ispH

GO Terms:

GO:0019288

CD Domains:

Go To Gene Page:

28326
31032 DUF2214

31032 - DUF2214

GO Terms:

NA

CD Domains:

Go To Gene Page:

31032
31108 PLN02205

31108 - PLN02205

GO Terms:

GO:0003825, GO:0005992, GO:0004805

CD Domains:

Go To Gene Page:

31108
31287 AAA_12

31287 - AAA_12

GO Terms:

NA

CD Domains:

Go To Gene Page:

31287
33169 Mpv17_PMP22

33169 - Mpv17_PMP22

GO Terms:

GO:0016021

CD Domains:

Go To Gene Page:

33169
33663 PLN02649

33663 - PLN02649

GO Terms:

GO:0004347, GO:0006094, GO:0006096

CD Domains:

Go To Gene Page:

33663
3462 hypothetical protein

3462 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3462
35408 PRK05134

35408 - PRK05134

GO Terms:

GO:0008757, GO:0008168, GO:0006744, GO:0008425, GO:0004395

CD Domains:

Go To Gene Page:

35408
37493 purU

37493 - purU

GO Terms:

GO:0009058, GO:0016742, GO:0006189, GO:0008864

CD Domains:

Go To Gene Page:

37493
3752 Abhydrolase_6

3752 - Abhydrolase_6

GO Terms:

GO:0003824, GO:0004177, GO:0006508

CD Domains:

Go To Gene Page:

3752
38575 carb_red_sniffer_like_SDR_c

38575 - carb_red_sniffer_like_SDR_c

GO Terms:

GO:0008152, GO:0016491, GO:0051341

CD Domains:

Go To Gene Page:

38575
4049 hypothetical protein

4049 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4049
40801 Trans_IPPS_HT

40801 - Trans_IPPS_HT

GO Terms:

GO:0008299, GO:0004659, GO:0004660, GO:0004661, GO:0004662, GO:0004663, GO:0008318, GO:0008412, GO:0008495, GO:0046428

CD Domains:

Go To Gene Page:

40801
6731 hypothetical protein

6731 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6731
9085 hypothetical protein

9085 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9085
9688 (Tp_bZIP7a/PAS) regulator [Rayko]

9688 - (Tp_bZIP7a/PAS) regulator [Rayko]

GO Terms:

GO:0004871, GO:0007165

CD Domains:

Go To Gene Page:

9688
GO ID Go Term p-value q-value Cluster
GO:0019288 mevalonate-independent isopentenyl diphosphate biosynthesis 0.0031011 1 Thaps_bicluster_0127
GO:0006744 ubiquinone biosynthesis 0.0031011 1 Thaps_bicluster_0127
GO:0005992 trehalose biosynthesis 0.00927638 1 Thaps_bicluster_0127
GO:0006563 L-serine metabolism 0.00927638 1 Thaps_bicluster_0127
GO:0006544 glycine metabolism 0.0123506 1 Thaps_bicluster_0127
GO:0006189 'de novo' IMP biosynthesis 0.0154159 1 Thaps_bicluster_0127
GO:0006094 gluconeogenesis 0.0275887 1 Thaps_bicluster_0127
GO:0008299 isoprenoid biosynthesis 0.0336223 1 Thaps_bicluster_0127
GO:0051341 regulation of oxidoreductase activity 0.0690961 1 Thaps_bicluster_0127
GO:0006096 glycolysis 0.108945 1 Thaps_bicluster_0127
Log in to post comments