Phatr_bicluster_0122 Residual: 0.44
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_0122 0.44 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_12674 nonhistone chromosomal protein (HMGB-UBF_HMG-box)

PHATRDRAFT_12674 - nonhistone chromosomal protein (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12674
PHATRDRAFT_14845 atp-dependent dnafamilyexpressed (recQ_fam)

PHATRDRAFT_14845 - atp-dependent dnafamilyexpressed (recQ_fam)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14845
PHATRDRAFT_15802 calmodulin-dependent protein kinase homologue (S_TKc)

PHATRDRAFT_15802 - calmodulin-dependent protein kinase homologue (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15802
PHATRDRAFT_16008 cytoplasmic dynein light chain 1 (Dynein_light superfamily)

PHATRDRAFT_16008 - cytoplasmic dynein light chain 1 (Dynein_light superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16008
PHATRDRAFT_22901 cathepsin a (Peptidase_S10)

PHATRDRAFT_22901 - cathepsin a (Peptidase_S10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22901
PHATRDRAFT_28882 (PLN02423)

PHATRDRAFT_28882 - (PLN02423)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28882
PHATRDRAFT_29658 nadh-cytochrome b-5 reductase (cyt_b5_reduct_like)

PHATRDRAFT_29658 - nadh-cytochrome b-5 reductase (cyt_b5_reduct_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29658
PHATRDRAFT_32339

PHATRDRAFT_32339 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32339
PHATRDRAFT_37571 kelch repeat protein

PHATRDRAFT_37571 - kelch repeat protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37571
PHATRDRAFT_37674 solute carrier family 22 (organic cation transporter)member 18 (MFS_1)

PHATRDRAFT_37674 - solute carrier family 22 (organic cation transporter)member 18 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37674
PHATRDRAFT_38924

PHATRDRAFT_38924 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38924
PHATRDRAFT_38977 beta-ketoacyl synthase

PHATRDRAFT_38977 - beta-ketoacyl synthase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38977
PHATRDRAFT_3924 ubiquitin carboxyl-terminal hydrolase isozyme l5 (Peptidase_C12_UCH37_BAP1)

PHATRDRAFT_3924 - ubiquitin carboxyl-terminal hydrolase isozyme l5 (Peptidase_C12_UCH37_BAP1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3924
PHATRDRAFT_39402 early-responsive to dehydration erd (DUF221 superfamily)

PHATRDRAFT_39402 - early-responsive to dehydration erd (DUF221 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39402
PHATRDRAFT_40044 astacin-like protein (PLN00052)

PHATRDRAFT_40044 - astacin-like protein (PLN00052)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40044
PHATRDRAFT_43881

PHATRDRAFT_43881 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43881
PHATRDRAFT_44485

PHATRDRAFT_44485 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44485
PHATRDRAFT_44586 hsf-type dna-binding domain containing protein (HSF_DNA-bind)

PHATRDRAFT_44586 - hsf-type dna-binding domain containing protein (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44586
PHATRDRAFT_45800 zinc-binding dehydrogenase family protein (MDR8)

PHATRDRAFT_45800 - zinc-binding dehydrogenase family protein (MDR8)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45800
PHATRDRAFT_48322 periplasmic binding protein

PHATRDRAFT_48322 - periplasmic binding protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48322
PHATRDRAFT_48364

PHATRDRAFT_48364 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48364
PHATRDRAFT_48559

PHATRDRAFT_48559 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48559
PHATRDRAFT_48560

PHATRDRAFT_48560 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48560
PHATRDRAFT_48951 tpr domain containing protein (TPR_12)

PHATRDRAFT_48951 - tpr domain containing protein (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48951
PHATRDRAFT_49320 peptidyl-prolyl cis-transcyclophilin type (cyclophilin)

PHATRDRAFT_49320 - peptidyl-prolyl cis-transcyclophilin type (cyclophilin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49320
PHATRDRAFT_49381 far-red impaired response protein

PHATRDRAFT_49381 - far-red impaired response protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49381
PHATRDRAFT_49958

PHATRDRAFT_49958 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49958
PHATRDRAFT_50287

PHATRDRAFT_50287 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50287
PHATRDRAFT_50330

PHATRDRAFT_50330 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50330
PHATRDRAFT_54612 dna repair protein (ERCC4)

PHATRDRAFT_54612 - dna repair protein (ERCC4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54612
PHATRDRAFT_55206 o-methyltransferase in d-chalcose pathway (AdoMet_MTases superfamily)

PHATRDRAFT_55206 - o-methyltransferase in d-chalcose pathway (AdoMet_MTases superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55206
GO ID Go Term p-value q-value Cluster
GO:0019307 mannose biosynthesis 0.00321067 1 Phatr_bicluster_0122
GO:0007017 microtubule-based process 0.00321067 1 Phatr_bicluster_0122
GO:0015904 tetracycline transport 0.0127857 1 Phatr_bicluster_0122
GO:0006259 DNA metabolism 0.0379055 1 Phatr_bicluster_0122
GO:0006511 ubiquitin-dependent protein catabolism 0.135415 1 Phatr_bicluster_0122
GO:0006355 regulation of transcription, DNA-dependent 0.153654 1 Phatr_bicluster_0122
GO:0006457 protein folding 0.317339 1 Phatr_bicluster_0122
GO:0006468 protein amino acid phosphorylation 0.431733 1 Phatr_bicluster_0122
GO:0006810 transport 0.466944 1 Phatr_bicluster_0122
GO:0006508 proteolysis and peptidolysis 0.523353 1 Phatr_bicluster_0122
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