Thaps_bicluster_0063 Residual: 0.47
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_0063 0.47 Thalassiosira pseudonana
Displaying 1 - 33 of 33
10216 hypothetical protein

10216 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10216
10942 DUF1255 superfamily

10942 - DUF1255 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

10942
11247 Methyltransf_7 superfamily

11247 - Methyltransf_7 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

11247
11943 hypothetical protein

11943 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11943
1515 (NIFU_1) NifU

1515 - (NIFU_1) NifU

GO Terms:

NA

CD Domains:

Go To Gene Page:

1515
1965 hypothetical protein

1965 - hypothetical protein

GO Terms:

GO:0031177, GO:0003910

CD Domains:

Go To Gene Page:

1965
22413 hypothetical protein

22413 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22413
22898 hypothetical protein

22898 - hypothetical protein

GO Terms:

GO:0004339

CD Domains:

Go To Gene Page:

22898
24248 CPSaseII_lrg

24248 - CPSaseII_lrg

GO Terms:

GO:0003824, GO:0004086, GO:0005524, GO:0006807, GO:0005737, GO:0006526, GO:0019856, GO:0008152, GO:0016874, GO:0009058

CD Domains:

Go To Gene Page:

24248
24935 hypothetical protein

24935 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24935
25560 PseudoU_synth_RluCD_like

25560 - PseudoU_synth_RluCD_like

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0004730

CD Domains:

Go To Gene Page:

25560
260974 MATE_like superfamily

260974 - MATE_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

260974
268552 AroE

268552 - AroE

GO Terms:

GO:0003855, GO:0009073, GO:0004764, GO:0005737, GO:0016089

CD Domains:

Go To Gene Page:

268552
269908 PRK12999

269908 - PRK12999

GO Terms:

GO:0003824, GO:0009374, GO:0005524, GO:0008152, GO:0016874, GO:0004736, GO:0005737, GO:0006094

CD Domains:

Go To Gene Page:

269908
270229 hypothetical protein

270229 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270229
28241 (gapC3) GapA

28241 - (gapC3) GapA

GO Terms:

GO:0004365, GO:0006096, GO:0051287, GO:0006006, GO:0008943

CD Domains:

Go To Gene Page:

28241
35180 Mpv17_PMP22

35180 - Mpv17_PMP22

GO Terms:

GO:0016021

CD Domains:

Go To Gene Page:

35180
40323 CPSaseII_lrg

40323 - CPSaseII_lrg

GO Terms:

GO:0003824, GO:0004086, GO:0005524, GO:0006807, GO:0005737, GO:0006526, GO:0019856, GO:0008152, GO:0016874, GO:0004087

CD Domains:

Go To Gene Page:

40323
428 FBP_aldolase_IIA

428 - FBP_aldolase_IIA

GO Terms:

GO:0004332, GO:0006096, GO:0008270

CD Domains:

Go To Gene Page:

428
5216 RluA

5216 - RluA

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0004730, GO:0016439

CD Domains:

Go To Gene Page:

5216
814 CdCA1

814 - CdCA1

GO Terms:

NA

CD Domains:

Go To Gene Page:

814
9749 hypothetical protein

9749 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9749
ThpsCp003 (petF) ferredoxin

ThpsCp003 - (petF) ferredoxin

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp003
ThpsCp009 (rbcL) ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

ThpsCp009 - (rbcL) ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp009
ThpsCp011 (ycf16) sulfate ABC transporter protein

ThpsCp011 - (ycf16) sulfate ABC transporter protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp011
ThpsCp034 (rpoB) RNA polymerase beta subunit

ThpsCp034 - (rpoB) RNA polymerase beta subunit

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp034
ThpsCp035 (rps20) ribosomal protein S20

ThpsCp035 - (rps20) ribosomal protein S20

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp035
ThpsCp036 (rpl33) ribosomal protein L33

ThpsCp036 - (rpl33) ribosomal protein L33

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp036
ThpsCp037 (rps18) ribosomal protein S18

ThpsCp037 - (rps18) ribosomal protein S18

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp037
ThpsCp043 (chlI) Mg-protoporyphyrin IX chelatase

ThpsCp043 - (chlI) Mg-protoporyphyrin IX chelatase

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp043
ThpsCp044 (psaM) photosystem I reaction center subunit M

ThpsCp044 - (psaM) photosystem I reaction center subunit M

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp044
ThpsCp127 (rps6) ribosomal protein S6

ThpsCp127 - (rps6) ribosomal protein S6

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp127
ThpsCt011 (trnY(gua))

ThpsCt011 - (trnY(gua))

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCt011
GO ID Go Term p-value q-value Cluster
GO:0019856 pyrimidine base biosynthesis 0.0000438 0.120381 Thaps_bicluster_0063
GO:0006526 arginine biosynthesis 0.000517768 1 Thaps_bicluster_0063
GO:0006807 nitrogen compound metabolism 0.000787334 1 Thaps_bicluster_0063
GO:0009152 purine ribonucleotide biosynthetic process 0.00392806 1 Thaps_bicluster_0063
GO:0016089 aromatic amino acid family biosynthesis, shikimate pathway 0.00784149 1 Thaps_bicluster_0063
GO:0006096 glycolysis 0.00897124 1 Thaps_bicluster_0063
GO:0006396 RNA processing 0.0212026 1 Thaps_bicluster_0063
GO:0009073 aromatic amino acid family biosynthesis 0.0271911 1 Thaps_bicluster_0063
GO:0006094 gluconeogenesis 0.0348304 1 Thaps_bicluster_0063
GO:0006006 glucose metabolism 0.0386288 1 Thaps_bicluster_0063
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