Phatr_bicluster_0163 Residual: 0.35
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_0163 0.35 Phaeodactylum tricornutum
Displaying 1 - 22 of 22
PHATRDRAFT_25218 abc transporter family protein (ABC_ATPase superfamily)

PHATRDRAFT_25218 - abc transporter family protein (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25218
PHATRDRAFT_32883

PHATRDRAFT_32883 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32883
PHATRDRAFT_36491

PHATRDRAFT_36491 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36491
PHATRDRAFT_36662

PHATRDRAFT_36662 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36662
PHATRDRAFT_42656

PHATRDRAFT_42656 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42656
PHATRDRAFT_43065 e2f transcription factor 2 (E2F_TDP)

PHATRDRAFT_43065 - e2f transcription factor 2 (E2F_TDP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43065
PHATRDRAFT_44661 (PAP2_C)

PHATRDRAFT_44661 - (PAP2_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44661
PHATRDRAFT_44788 arsenical pump family protein (P_permease)

PHATRDRAFT_44788 - arsenical pump family protein (P_permease)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44788
PHATRDRAFT_45402 polymorphic outer membrane protein

PHATRDRAFT_45402 - polymorphic outer membrane protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45402
PHATRDRAFT_45439

PHATRDRAFT_45439 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45439
PHATRDRAFT_45471

PHATRDRAFT_45471 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45471
PHATRDRAFT_45509 glutamine-dependent nad(+)essential for the formation of nad(+) from nicotinic acid adenine dinucleotide (PLN02339)

PHATRDRAFT_45509 - glutamine-dependent nad(+)essential for the formation of nad(+) from nicotinic acid adenine dinucleotide (PLN02339)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45509
PHATRDRAFT_45570 yo87_caeel uncharacterized protein (DDRGK)

PHATRDRAFT_45570 - yo87_caeel uncharacterized protein (DDRGK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45570
PHATRDRAFT_46112

PHATRDRAFT_46112 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46112
PHATRDRAFT_46511

PHATRDRAFT_46511 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46511
PHATRDRAFT_47007

PHATRDRAFT_47007 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47007
PHATRDRAFT_48626

PHATRDRAFT_48626 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48626
PHATRDRAFT_49200

PHATRDRAFT_49200 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49200
PHATRDRAFT_5288 tpr repeat (TPR_12)

PHATRDRAFT_52685 - tpr repeat (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52685
PHATRDRAFT_54703 (AANH_like superfamily)

PHATRDRAFT_5288 - (AANH_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5288
PHATRDRAFT_5532 udp-n-acteylglucosamine pyrophosphorylase 1 (UDPGlcNAc_PPase)

PHATRDRAFT_54703 - udp-n-acteylglucosamine pyrophosphorylase 1 (UDPGlcNAc_PPase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54703

PHATRDRAFT_5532 - n6-dna methyltransferase a (HemK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_5532
GO ID Go Term p-value q-value Cluster
GO:0009435 NAD biosynthesis 0.00197506 1 Phatr_bicluster_0163
GO:0006807 nitrogen compound metabolism 0.0137641 1 Phatr_bicluster_0163
GO:0000074 regulation of cell cycle 0.03318 1 Phatr_bicluster_0163
GO:0006355 regulation of transcription, DNA-dependent 0.199489 1 Phatr_bicluster_0163
Log in to post comments