Phatr_bicluster_0003 Residual: 0.71
Phaeodactylum tricornutum

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
Phatr_bicluster_0003 0.71 Phaeodactylum tricornutum
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Displaying 1 - 25 of 25
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PHATRDRAFT_15393 protoplast secreted protein 2 precursor (FMN_red superfamily)

PHATRDRAFT_15393 - protoplast secreted protein 2 precursor (FMN_red superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15393
PHATRDRAFT_33435 fatty acid hydroxylase (FA_hydroxylase)

PHATRDRAFT_33435 - fatty acid hydroxylase (FA_hydroxylase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33435
PHATRDRAFT_34710 ankyrin repeat (ANK)

PHATRDRAFT_34710 - ankyrin repeat (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34710
PHATRDRAFT_35058 periplasmic binding protein (TroA-like superfamily)

PHATRDRAFT_35058 - periplasmic binding protein (TroA-like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35058
PHATRDRAFT_3656 disease resistance protein

PHATRDRAFT_3656 - disease resistance protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3656
PHATRDRAFT_37602

PHATRDRAFT_37602 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37602
PHATRDRAFT_38581 notch homologtranslocation-associated

PHATRDRAFT_38581 - notch homologtranslocation-associated

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38581
PHATRDRAFT_39151 pyrimidine-nucleoside phosphorylase (Y_phosphoryl)

PHATRDRAFT_39151 - pyrimidine-nucleoside phosphorylase (Y_phosphoryl)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39151
PHATRDRAFT_40861

PHATRDRAFT_40861 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40861
PHATRDRAFT_43799 glutathione-dependent formaldehyde-gfa (COG3791)

PHATRDRAFT_43799 - glutathione-dependent formaldehyde-gfa (COG3791)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43799
PHATRDRAFT_44046 ankyrin repeat family protein (ANK)

PHATRDRAFT_44046 - ankyrin repeat family protein (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44046
PHATRDRAFT_45140 monooxygenase fad-binding (NAD_binding_8 superfamily)

PHATRDRAFT_45140 - monooxygenase fad-binding (NAD_binding_8 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45140
PHATRDRAFT_45338

PHATRDRAFT_45338 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45338
PHATRDRAFT_45551 (LPLAT_LCLAT1-like)

PHATRDRAFT_45551 - (LPLAT_LCLAT1-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45551
PHATRDRAFT_46237 probable bacterial hemoglobin (globin)

PHATRDRAFT_46237 - probable bacterial hemoglobin (globin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46237
PHATRDRAFT_47774

PHATRDRAFT_47774 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47774
PHATRDRAFT_48678 atrial natriuretic peptide receptor (CHD)

PHATRDRAFT_48678 - atrial natriuretic peptide receptor (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48678
PHATRDRAFT_48999 transmembrane transport protein (LldP)

PHATRDRAFT_48999 - transmembrane transport protein (LldP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48999
PHATRDRAFT_49202

PHATRDRAFT_49202 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49202
PHATRDRAFT_49506 high mobility group (HMGB-UBF_HMG-box)

PHATRDRAFT_49506 - high mobility group (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49506
PHATRDRAFT_49555 guanylyl cyclase family member (gcy-28) (CHD)

PHATRDRAFT_49555 - guanylyl cyclase family member (gcy-28) (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49555
PHATRDRAFT_49887

PHATRDRAFT_49887 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49887
PHATRDRAFT_49989 (zf-MYND)

PHATRDRAFT_49989 - (zf-MYND)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49989
PHATRDRAFT_54151 long-chain fatty-acid-ligase (FAA1)

PHATRDRAFT_54151 - long-chain fatty-acid-ligase (FAA1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54151
PHATRDRAFT_6066 gaf domain (DUF2453)

PHATRDRAFT_6066 - gaf domain (DUF2453)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6066
GO ID Go Term p-value q-value Cluster
GO:0009190 cyclic nucleotide biosynthesis 0.00106853 1 Phatr_bicluster_0003
GO:0015727 lactate transport 0.00296369 1 Phatr_bicluster_0003
GO:0007242 intracellular signaling cascade 0.00649175 1 Phatr_bicluster_0003
GO:0006206 pyrimidine base metabolism 0.0118065 1 Phatr_bicluster_0003
GO:0008152 metabolism 0.051036 1 Phatr_bicluster_0003
GO:0007165 signal transduction 0.130903 1 Phatr_bicluster_0003
GO:0006810 transport 0.440472 1 Phatr_bicluster_0003
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0003
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