Phatr_bicluster_0165 Residual: 0.45
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_0165 0.45 Phaeodactylum tricornutum
Displaying 1 - 34 of 34
PHATRDRAFT_1389 disease resistance protein

PHATRDRAFT_1389 - disease resistance protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1389
PHATRDRAFT_20948 cytochrome c isoform 1 (Cytochrom_C superfamily)

PHATRDRAFT_20948 - cytochrome c isoform 1 (Cytochrom_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20948
PHATRDRAFT_32294 light-harvesting protein (Chloroa_b-bind)

PHATRDRAFT_32294 - light-harvesting protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32294
PHATRDRAFT_33054

PHATRDRAFT_33054 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33054
PHATRDRAFT_33704

PHATRDRAFT_33704 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33704
PHATRDRAFT_34431 (LRR_RI superfamily)

PHATRDRAFT_34431 - (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34431
PHATRDRAFT_36711 spentranscriptional regulator

PHATRDRAFT_36175 - spentranscriptional regulator

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36175
PHATRDRAFT_37567 family with sequence similaritymember a (DUF842 superfamily)

PHATRDRAFT_36711 - family with sequence similaritymember a (DUF842 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36711
PHATRDRAFT_37575

PHATRDRAFT_37567 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37567
PHATRDRAFT_39443

PHATRDRAFT_37575 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37575
PHATRDRAFT_4014

PHATRDRAFT_39443 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39443
PHATRDRAFT_41570 peptidase family s49 protein (S49_Sppa_N_C)

PHATRDRAFT_4014 - peptidase family s49 protein (S49_Sppa_N_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4014
PHATRDRAFT_43498 fatty acid desaturase family member (fat-2) (Membrane-FADS-like superfamily)

PHATRDRAFT_41570 - fatty acid desaturase family member (fat-2) (Membrane-FADS-like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41570
PHATRDRAFT_44232 tethering factor sec34

PHATRDRAFT_43498 - tethering factor sec34

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43498
PHATRDRAFT_44959

PHATRDRAFT_43971 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43971
PHATRDRAFT_44994 atp-dependent clp protease (S14_ClpP_2)

PHATRDRAFT_44232 - atp-dependent clp protease (S14_ClpP_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44232
PHATRDRAFT_45238 dnaj heat shock n-terminal domain-containing protein (DnaJ)

PHATRDRAFT_44959 - dnaj heat shock n-terminal domain-containing protein (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44959
PHATRDRAFT_45527 thrombospondin type 3 repeat:cna b-type

PHATRDRAFT_44994 - thrombospondin type 3 repeat:cna b-type

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44994
PHATRDRAFT_46165 uncharacterized conserved protein (SPOUT_MTase superfamily)

PHATRDRAFT_45238 - uncharacterized conserved protein (SPOUT_MTase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45238
PHATRDRAFT_47099 pomp cg9324-pa (UMP1 superfamily)

PHATRDRAFT_45527 - pomp cg9324-pa (UMP1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45527
PHATRDRAFT_47752

PHATRDRAFT_46165 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46165
PHATRDRAFT_47766 conserved protein having 3 transmembrane domains and possible er retention motif possible er protein (Sec62 superfamily)

PHATRDRAFT_47099 - conserved protein having 3 transmembrane domains and possible er retention motif possible er protein (Sec62 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47099
PHATRDRAFT_48128 chromosome segregation atpase

PHATRDRAFT_47752 - chromosome segregation atpase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47752
PHATRDRAFT_48867 tpr domain containing protein (TPR)

PHATRDRAFT_47766 - tpr domain containing protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47766
PHATRDRAFT_50191 serine arginine repetitive matrix 1

PHATRDRAFT_48128 - serine arginine repetitive matrix 1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48128
PHATRDRAFT_54019 nucleosomal binding protein

PHATRDRAFT_48867 - nucleosomal binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48867
PHATRDRAFT_54065

PHATRDRAFT_50191 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50191
PHATRDRAFT_54217 heat shock protein 70 (PTZ00009)

PHATRDRAFT_54019 - heat shock protein 70 (PTZ00009)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54019
PHATRDRAFT_54465 fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

PHATRDRAFT_54065 - fucoxanthin chlorophyll a c binding protein (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54065
PHATRDRAFT_8282

PHATRDRAFT_54217 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54217
PHATRDRAFT_9320

PHATRDRAFT_54465 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54465
PHATRDRAFT_9547 nucleosome binding protein

PHATRDRAFT_8282 - nucleosome binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8282

PHATRDRAFT_9320 - mgc82894 protein (Rpn3_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9320

PHATRDRAFT_9547 - replication factor c (activator 1) 4 (rfc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9547
GO ID Go Term p-value q-value Cluster
GO:0006636 fatty acid desaturation 0.0244517 1 Phatr_bicluster_0165
GO:0006260 DNA replication 0.0624567 1 Phatr_bicluster_0165
GO:0015031 protein transport 0.074057 1 Phatr_bicluster_0165
GO:0009765 photosynthesis light harvesting 0.0923489 1 Phatr_bicluster_0165
GO:0006508 proteolysis and peptidolysis 0.1023 1 Phatr_bicluster_0165
GO:0006457 protein folding 0.254387 1 Phatr_bicluster_0165
GO:0006468 protein amino acid phosphorylation 0.352461 1 Phatr_bicluster_0165
GO:0006355 regulation of transcription, DNA-dependent 0.426896 1 Phatr_bicluster_0165
GO:0006118 electron transport 0.441702 1 Phatr_bicluster_0165
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