Phatr_bicluster_0192 Residual: 0.20
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_0192 0.20 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_11652 translation initiation factor if-3 (infC)

PHATRDRAFT_11652 - translation initiation factor if-3 (infC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11652
PHATRDRAFT_11653 nucleolar essential protein 1 (EMG1)

PHATRDRAFT_11653 - nucleolar essential protein 1 (EMG1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11653
PHATRDRAFT_12140 chaperonedomain protein (DnaJ)

PHATRDRAFT_12140 - chaperonedomain protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12140
PHATRDRAFT_12896 ogd prolylhydroxylase domainfe ii 2- (Ofd1_CTDD)

PHATRDRAFT_12896 - ogd prolylhydroxylase domainfe ii 2- (Ofd1_CTDD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12896
PHATRDRAFT_12925 sumt_schpo probable uroporphyrinogen-iii c-methyltransferase (SUMT)

PHATRDRAFT_12925 - sumt_schpo probable uroporphyrinogen-iii c-methyltransferase (SUMT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12925
PHATRDRAFT_13281 mgc83122 protein (NIP7)

PHATRDRAFT_13281 - mgc83122 protein (NIP7)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13281
PHATRDRAFT_14176 transducin family protein wd-40 repeat family protein (WD40)

PHATRDRAFT_14176 - transducin family protein wd-40 repeat family protein (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14176
PHATRDRAFT_20773 loc733436 protein (CBF5)

PHATRDRAFT_20773 - loc733436 protein (CBF5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20773
PHATRDRAFT_2097 atp-dependent rna helicase ded1 (DEADc)

PHATRDRAFT_2097 - atp-dependent rna helicase ded1 (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2097
PHATRDRAFT_31987 density regulated protein drp1 (DENR_C)

PHATRDRAFT_31987 - density regulated protein drp1 (DENR_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31987
PHATRDRAFT_33896 homeobox protein (PHD)

PHATRDRAFT_33896 - homeobox protein (PHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33896
PHATRDRAFT_34358

PHATRDRAFT_34358 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34358
PHATRDRAFT_34363

PHATRDRAFT_34363 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34363
PHATRDRAFT_34956 g1 s-specific cyclin-e (COG5024)

PHATRDRAFT_34956 - g1 s-specific cyclin-e (COG5024)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34956
PHATRDRAFT_34984 thyroid hormone receptor interactor 3

PHATRDRAFT_34984 - thyroid hormone receptor interactor 3

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34984
PHATRDRAFT_35395 cytochrome b5 (Cyt-b5)

PHATRDRAFT_35395 - cytochrome b5 (Cyt-b5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35395
PHATRDRAFT_37283 phosphoribosylglycinamide synthetase family protein (PRK07206)

PHATRDRAFT_37283 - phosphoribosylglycinamide synthetase family protein (PRK07206)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37283
PHATRDRAFT_42844 tiny fragments locus 9c (TrmA)

PHATRDRAFT_42844 - tiny fragments locus 9c (TrmA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42844
PHATRDRAFT_42926 programmed cell death 2-like (PDCD2_C superfamily)

PHATRDRAFT_42926 - programmed cell death 2-like (PDCD2_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42926
PHATRDRAFT_43501

PHATRDRAFT_43501 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43501
PHATRDRAFT_44395 (RRM)

PHATRDRAFT_44395 - (RRM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44395
PHATRDRAFT_44643

PHATRDRAFT_44643 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44643
PHATRDRAFT_45289

PHATRDRAFT_45289 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45289
PHATRDRAFT_45828 sda1 domain containing 1 (SDA1)

PHATRDRAFT_45828 - sda1 domain containing 1 (SDA1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45828
PHATRDRAFT_45855 oxidoreductase-like protein (FabG)

PHATRDRAFT_45855 - oxidoreductase-like protein (FabG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45855
PHATRDRAFT_46385 y2987_anasp upf0187 protein alr2987 (Bestrophin superfamily)

PHATRDRAFT_46385 - y2987_anasp upf0187 protein alr2987 (Bestrophin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46385
PHATRDRAFT_46671

PHATRDRAFT_46671 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46671
PHATRDRAFT_46676

PHATRDRAFT_46676 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46676
PHATRDRAFT_46837 nop14_mousenucleolar protein 14 (nucleolar complex protein 14) (Nop14)

PHATRDRAFT_46837 - nop14_mousenucleolar protein 14 (nucleolar complex protein 14) (Nop14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46837
PHATRDRAFT_47014 rna binding s1 domain protein (S1_like)

PHATRDRAFT_47014 - rna binding s1 domain protein (S1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47014
PHATRDRAFT_49586 phd-finger familyexpressed (RING)

PHATRDRAFT_49586 - phd-finger familyexpressed (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49586
PHATRDRAFT_4974 transducin wd-40 repeat protein (WD40 superfamily)

PHATRDRAFT_4974 - transducin wd-40 repeat protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4974
GO ID Go Term p-value q-value Cluster
GO:0006915 apoptosis 0.00886694 1 Phatr_bicluster_0192
GO:0008152 metabolism 0.595805 1 Phatr_bicluster_0192
GO:0006779 porphyrin biosynthesis 0.0292769 1 Phatr_bicluster_0192
GO:0006457 protein folding 0.296964 1 Phatr_bicluster_0192
GO:0019538 protein metabolism 0.101759 1 Phatr_bicluster_0192
GO:0016567 protein ubiquitination 0.193944 1 Phatr_bicluster_0192
GO:0000074 regulation of cell cycle 0.0963646 1 Phatr_bicluster_0192
GO:0006355 regulation of transcription, DNA-dependent 0.487367 1 Phatr_bicluster_0192
GO:0007046 ribosome biogenesis 0.00886694 1 Phatr_bicluster_0192
GO:0006396 RNA processing 0.1541 1 Phatr_bicluster_0192
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