Phatr_bicluster_0222 Residual: 0.32
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_0222 0.32 Phaeodactylum tricornutum
Displaying 1 - 24 of 24
PHATRDRAFT_11673 band 7 family protein (SPFH_like_u4)

PHATRDRAFT_11673 - band 7 family protein (SPFH_like_u4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11673
PHATRDRAFT_28743 wdr82 protein (WD40 superfamily)

PHATRDRAFT_28743 - wdr82 protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28743
PHATRDRAFT_33651 cral trio cell signalling protein (SEC14)

PHATRDRAFT_33651 - cral trio cell signalling protein (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33651
PHATRDRAFT_34295

PHATRDRAFT_34295 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34295
PHATRDRAFT_36891 (R3H superfamily)

PHATRDRAFT_36891 - (R3H superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36891
PHATRDRAFT_40347

PHATRDRAFT_40347 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40347
PHATRDRAFT_41659 atp-dependent transporter (Uup)

PHATRDRAFT_41659 - atp-dependent transporter (Uup)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41659
PHATRDRAFT_42948 viral a-type inclusion

PHATRDRAFT_42948 - viral a-type inclusion

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42948
PHATRDRAFT_43226 n-terminal domain containing protein

PHATRDRAFT_43226 - n-terminal domain containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43226
PHATRDRAFT_44351 mpt family transporter: inner membrane translocasetim44 (Tim44 superfamily)

PHATRDRAFT_44351 - mpt family transporter: inner membrane translocasetim44 (Tim44 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44351
PHATRDRAFT_44427 glucose-repressible alcohol dehydrogenase transcriptional effector ccr4 and related proteins (EEP superfamily)

PHATRDRAFT_44427 - glucose-repressible alcohol dehydrogenase transcriptional effector ccr4 and related proteins (EEP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44427
PHATRDRAFT_44473 deacetylase sulfotransferase

PHATRDRAFT_44473 - deacetylase sulfotransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44473
PHATRDRAFT_44526 (alpha_CA superfamily)

PHATRDRAFT_44526 - (alpha_CA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44526
PHATRDRAFT_48427

PHATRDRAFT_48427 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48427
PHATRDRAFT_48720 ccr4 associated factor-like protein

PHATRDRAFT_48720 - ccr4 associated factor-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48720
PHATRDRAFT_48786 tpr-repeat containing protein (TPR)

PHATRDRAFT_48786 - tpr-repeat containing protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48786
PHATRDRAFT_49026 (Glyco_trans_2_3)

PHATRDRAFT_49026 - (Glyco_trans_2_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49026
PHATRDRAFT_49385 deoxycytidyl transferase (PolY superfamily)

PHATRDRAFT_49385 - deoxycytidyl transferase (PolY superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49385
PHATRDRAFT_49664

PHATRDRAFT_49664 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49664
PHATRDRAFT_54411 sugar (d-ribose) abc transporter (periplasmic binding protein) (Peripla_BP_4)

PHATRDRAFT_54411 - sugar (d-ribose) abc transporter (periplasmic binding protein) (Peripla_BP_4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54411
PHATRDRAFT_708 yk16_schpoatp-dependent rna helicase (HrpA)

PHATRDRAFT_708 - yk16_schpoatp-dependent rna helicase (HrpA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_708
PHATRDRAFT_7114 tim22_yarli mitochondrial import inner membrane translocase subunit tim22 (Tim17)

PHATRDRAFT_7114 - tim22_yarli mitochondrial import inner membrane translocase subunit tim22 (Tim17)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7114
PHATRDRAFT_8982 phosphoglycerate mutase (HP_PGM_like)

PHATRDRAFT_8982 - phosphoglycerate mutase (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8982
PHATRDRAFT_9879 haloacid dehalogenase-like hydrolase (HAD superfamily)

PHATRDRAFT_9879 - haloacid dehalogenase-like hydrolase (HAD superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9879
GO ID Go Term p-value q-value Cluster
GO:0006730 one-carbon compound metabolism 0.00886476 1 Phatr_bicluster_0222
GO:0015031 protein transport 0.066897 1 Phatr_bicluster_0222
GO:0006281 DNA repair 0.0731548 1 Phatr_bicluster_0222
GO:0000074 regulation of cell cycle 0.0731548 1 Phatr_bicluster_0222
GO:0006096 glycolysis 0.0752324 1 Phatr_bicluster_0222
GO:0006886 intracellular protein transport 0.0855585 1 Phatr_bicluster_0222
GO:0006396 RNA processing 0.117917 1 Phatr_bicluster_0222
GO:0006810 transport 0.352949 1 Phatr_bicluster_0222
GO:0008152 metabolism 0.492943 1 Phatr_bicluster_0222
Log in to post comments