Thaps_bicluster_0239 Residual: 0.34
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_0239 0.34 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 26 of 26
" class="views-fluidgrid-wrapper clear-block">
10943 (DXR1) PLN02696

10943 - (DXR1) PLN02696

GO Terms:

GO:0003824, GO:0008299, GO:0030604

CD Domains:

Go To Gene Page:

10943
1539 hypothetical protein

1539 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1539
16169 TPP_E1_PDC_ADC_BCADC

16169 - TPP_E1_PDC_ADC_BCADC

GO Terms:

GO:0008152, GO:0016624, GO:0004739

CD Domains:

Go To Gene Page:

16169
21989 (Tp_bZIP15) regulator [Rayko]

21989 - (Tp_bZIP15) regulator [Rayko]

GO Terms:

GO:0003677, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

21989
23291 hypothetical protein

23291 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23291
24832 hypothetical protein

24832 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24832
25097 PRK05427

25097 - PRK05427

GO Terms:

GO:0005737, GO:0016462

CD Domains:

Go To Gene Page:

25097
2611 hypothetical protein

2611 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2611
263714 LPLAT_GPAT

263714 - LPLAT_GPAT

GO Terms:

GO:0008152, GO:0008415

CD Domains:

Go To Gene Page:

263714
264387 MATE_like superfamily

264387 - MATE_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

264387
268270 Patched

268270 - Patched

GO Terms:

GO:0008158, GO:0016020

CD Domains:

Go To Gene Page:

268270
269393 (SQDB1) PLN02572

269393 - (SQDB1) PLN02572

GO Terms:

GO:0046507

CD Domains:

Go To Gene Page:

269393
270312 hypothetical protein

270312 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270312
270396 hypothetical protein

270396 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270396
2892 tsf

2892 - tsf

GO Terms:

GO:0003746, GO:0006414

CD Domains:

Go To Gene Page:

2892
3143 (DES9) Delta12-FADS-like

3143 - (DES9) Delta12-FADS-like

GO Terms:

GO:0016491, GO:0006636, GO:0016020, GO:0016717, GO:0016215, GO:0018688, GO:0018689, GO:0042389

CD Domains:

Go To Gene Page:

3143
31446 hypothetical protein

31446 - hypothetical protein

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

31446
36669 TPT

36669 - TPT

GO Terms:

NA

CD Domains:

Go To Gene Page:

36669
36684 PRK10416

36684 - PRK10416

GO Terms:

GO:0003723, GO:0005525, GO:0005786, GO:0006614, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

36684
40001 PRK05433

40001 - PRK05433

GO Terms:

GO:0005525, GO:0006412, GO:0007264, GO:0003924, GO:0008547

CD Domains:

Go To Gene Page:

40001
40725 (cdc48-2) CDC48
4387 Mito_carr

4387 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005743

CD Domains:

Go To Gene Page:

4387
5078 PLN02530

5078 - PLN02530

GO Terms:

GO:0004812, GO:0005524, GO:0006418, GO:0006412, GO:0004821, GO:0005737, GO:0006427

CD Domains:

Go To Gene Page:

5078
7230 SGL

7230 - SGL

GO Terms:

NA

CD Domains:

Go To Gene Page:

7230
8119 hypothetical protein

8119 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8119
9918 hypothetical protein

9918 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9918
GO ID Go Term p-value q-value Cluster
GO:0006636 fatty acid desaturation 0.034223 1 Thaps_bicluster_0239
GO:0006427 histidyl-tRNA aminoacylation 0.00578093 1 Thaps_bicluster_0239
GO:0008299 isoprenoid biosynthesis 0.0314132 1 Thaps_bicluster_0239
GO:0008152 metabolism 0.332159 1 Thaps_bicluster_0239
GO:0006412 protein biosynthesis 0.010932 1 Thaps_bicluster_0239
GO:0006355 regulation of transcription, DNA-dependent 0.6012 1 Thaps_bicluster_0239
GO:0007264 small GTPase mediated signal transduction 0.0941568 1 Thaps_bicluster_0239
GO:0006614 SRP-dependent cotranslational protein-membrane targeting 0.0172498 1 Thaps_bicluster_0239
GO:0006414 translational elongation 0.034223 1 Thaps_bicluster_0239
GO:0006810 transport 0.419404 1 Thaps_bicluster_0239
Log in to post comments