Phatr_bicluster_0004 Residual: 0.65
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_0004 0.65 Phaeodactylum tricornutum
Displaying 1 - 40 of 40
PHATRDRAFT_14808 nud24_arath nudix hydrolasechloroplast precursor (Nudix_Hydrolase superfamily)

PHATRDRAFT_14808 - nud24_arath nudix hydrolasechloroplast precursor (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14808
PHATRDRAFT_15968 (PLN02906)

PHATRDRAFT_15968 - (PLN02906)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15968
PHATRDRAFT_16021 (SmpB)

PHATRDRAFT_16021 - (SmpB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16021
PHATRDRAFT_21736 at3g26060 mpe11_21 (PRX_BCP)

PHATRDRAFT_21736 - at3g26060 mpe11_21 (PRX_BCP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21736
PHATRDRAFT_2215 at3g11670 t19f11_7 (Glycos_transf_1 superfamily)

PHATRDRAFT_2215 - at3g11670 t19f11_7 (Glycos_transf_1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2215
PHATRDRAFT_22274 long chain polyunsaturated fatty acid elongation (ELO)

PHATRDRAFT_22274 - long chain polyunsaturated fatty acid elongation (ELO)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22274
PHATRDRAFT_23598 glyceraldehyde-3-phosphate dehydrogenase (PRK08955)

PHATRDRAFT_23598 - glyceraldehyde-3-phosphate dehydrogenase (PRK08955)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23598
PHATRDRAFT_33329 zinc-containing alcohol dehydrogenase superfamily (CAD1)

PHATRDRAFT_30246 - zinc-containing alcohol dehydrogenase superfamily (CAD1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_30246
PHATRDRAFT_33637 prolyl 4-expressed (P4Hc)

PHATRDRAFT_33329 - prolyl 4-expressed (P4Hc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33329
PHATRDRAFT_37402

PHATRDRAFT_33637 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33637
PHATRDRAFT_38497

PHATRDRAFT_37402 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37402
PHATRDRAFT_39480

PHATRDRAFT_38497 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38497
PHATRDRAFT_39786 glycosyl transferase (Gly_transf_sug superfamily)

PHATRDRAFT_39480 - glycosyl transferase (Gly_transf_sug superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39480
PHATRDRAFT_40151 hsf protein (HSF_DNA-bind)

PHATRDRAFT_39786 - hsf protein (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39786
PHATRDRAFT_40515

PHATRDRAFT_40151 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40151
PHATRDRAFT_40662

PHATRDRAFT_40515 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40515
PHATRDRAFT_41004

PHATRDRAFT_40662 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40662
PHATRDRAFT_41318 (TPR)

PHATRDRAFT_41004 - (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41004
PHATRDRAFT_41386

PHATRDRAFT_41318 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41318
PHATRDRAFT_41628

PHATRDRAFT_41386 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41386
PHATRDRAFT_43105

PHATRDRAFT_41628 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41628
PHATRDRAFT_43826 pde318 (pigment defective 318) gtp binding (COG1084)

PHATRDRAFT_43105 - pde318 (pigment defective 318) gtp binding (COG1084)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43105
PHATRDRAFT_44177 receptor guanylyl cyclase gc-ii (CHD)

PHATRDRAFT_43826 - receptor guanylyl cyclase gc-ii (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43826
PHATRDRAFT_44725 cog0737: 5-nucleotidase 2-cyclic phosphodiesterase and related esterases (MPP_superfamily superfamily)

PHATRDRAFT_44177 - cog0737: 5-nucleotidase 2-cyclic phosphodiesterase and related esterases (MPP_superfamily superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44177
PHATRDRAFT_45392

PHATRDRAFT_44725 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44725
PHATRDRAFT_45591 heat shock factor (HSF_DNA-bind superfamily)

PHATRDRAFT_45392 - heat shock factor (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45392
PHATRDRAFT_45934

PHATRDRAFT_45591 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45591
PHATRDRAFT_46977 e1a binding protein p400 (HSA)

PHATRDRAFT_45934 - e1a binding protein p400 (HSA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45934
PHATRDRAFT_47298

PHATRDRAFT_46977 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46977
PHATRDRAFT_47927

PHATRDRAFT_47298 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47298
PHATRDRAFT_48040

PHATRDRAFT_47927 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47927
PHATRDRAFT_48049 (Abhydrolase_6)

PHATRDRAFT_48040 - (Abhydrolase_6)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48040
PHATRDRAFT_48307 epsilon frustilin

PHATRDRAFT_48049 - epsilon frustilin

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48049
PHATRDRAFT_49663 homocysteine s-methyltransferase family protein (MHT1)

PHATRDRAFT_48307 - homocysteine s-methyltransferase family protein (MHT1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48307
PHATRDRAFT_50012 helicase domain protein (HA)

PHATRDRAFT_49663 - helicase domain protein (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49663
PHATRDRAFT_50187 na+ solute symporter (SLC5-6-like_sbd superfamily)

PHATRDRAFT_50012 - na+ solute symporter (SLC5-6-like_sbd superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50012
PHATRDRAFT_50251

PHATRDRAFT_50187 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50187
PHATRDRAFT_50428 cyclin d1

PHATRDRAFT_50251 - cyclin d1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50251
PHATRDRAFT_54979 retinal guanylate cyclase (CHD)

PHATRDRAFT_50428 - retinal guanylate cyclase (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50428

PHATRDRAFT_54979 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54979
GO ID Go Term p-value q-value Cluster
GO:0009190 cyclic nucleotide biosynthesis 0.0024406 1 Phatr_bicluster_0004
GO:0007242 intracellular signaling cascade 0.0144685 1 Phatr_bicluster_0004
GO:0007165 signal transduction 0.0179288 1 Phatr_bicluster_0004
GO:0006006 glucose metabolism 0.0307293 1 Phatr_bicluster_0004
GO:0006564 L-serine biosynthesis 0.0350457 1 Phatr_bicluster_0004
GO:0000074 regulation of cell cycle 0.141104 1 Phatr_bicluster_0004
GO:0006096 glycolysis 0.144955 1 Phatr_bicluster_0004
GO:0019538 protein metabolism 0.148789 1 Phatr_bicluster_0004
GO:0006310 DNA recombination 0.152607 1 Phatr_bicluster_0004
GO:0006355 regulation of transcription, DNA-dependent 0.254081 1 Phatr_bicluster_0004
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