Phatr_bicluster_0095 Residual: 0.39
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_0095 0.39 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_11230 like protein (BolA)

PHATRDRAFT_11230 - like protein (BolA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11230
PHATRDRAFT_12927 (LRR_RI superfamily)

PHATRDRAFT_12927 - (LRR_RI superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12927
PHATRDRAFT_14599 rna polymerase sigma factor (Sig70-cyanoRpoD)

PHATRDRAFT_14599 - rna polymerase sigma factor (Sig70-cyanoRpoD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14599
PHATRDRAFT_14867 uncharacterized conserved protein (Fe-S_biosyn superfamily)

PHATRDRAFT_14867 - uncharacterized conserved protein (Fe-S_biosyn superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14867
PHATRDRAFT_1598 hippocampus abundant gene transcript 1 (MFS_1)

PHATRDRAFT_1598 - hippocampus abundant gene transcript 1 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1598
PHATRDRAFT_16076 at3g50680 t3a5_60

PHATRDRAFT_16076 - at3g50680 t3a5_60

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16076
PHATRDRAFT_16334 at3g61870 f21f14_40 (DUF4079)

PHATRDRAFT_16334 - at3g61870 f21f14_40 (DUF4079)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16334
PHATRDRAFT_19030 mc family transporter: phosphate (Mito_carr)

PHATRDRAFT_19030 - mc family transporter: phosphate (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19030
PHATRDRAFT_2217 histidine decarboxylase (PLN03032)

PHATRDRAFT_2217 - histidine decarboxylase (PLN03032)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_2217
PHATRDRAFT_33463

PHATRDRAFT_33412 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33412
PHATRDRAFT_37144 short-chain alcohol dehydrogenase-like protein (NADB_Rossmann superfamily)

PHATRDRAFT_33463 - short-chain alcohol dehydrogenase-like protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33463
PHATRDRAFT_37545 rna polymerase ii transcriptional (PC4)

PHATRDRAFT_37144 - rna polymerase ii transcriptional (PC4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37144
PHATRDRAFT_38963

PHATRDRAFT_37545 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37545
PHATRDRAFT_41409 rna helicase - like protein (Dtyr_deacylase superfamily)

PHATRDRAFT_38963 - rna helicase - like protein (Dtyr_deacylase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38963
PHATRDRAFT_44383 (NADB_Rossmann superfamily)

PHATRDRAFT_41409 - (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41409
PHATRDRAFT_44612 eif4g-related protein nat1 (W2_eIF4G1_like)

PHATRDRAFT_44383 - eif4g-related protein nat1 (W2_eIF4G1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44383
PHATRDRAFT_44751

PHATRDRAFT_44612 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44612
PHATRDRAFT_45205 ribonuclease h i (RNase_HI_like)

PHATRDRAFT_44751 - ribonuclease h i (RNase_HI_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44751
PHATRDRAFT_45926

PHATRDRAFT_45205 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45205
PHATRDRAFT_4604 heat shock factor (HSF_DNA-bind superfamily)

PHATRDRAFT_45926 - heat shock factor (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45926
PHATRDRAFT_46218 af375428_1at4g29590 t16l4_100

PHATRDRAFT_4604 - af375428_1at4g29590 t16l4_100

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4604
PHATRDRAFT_46990

PHATRDRAFT_46218 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46218
PHATRDRAFT_47959 aldo keto reductase family protein (Aldo_ket_red)

PHATRDRAFT_46990 - aldo keto reductase family protein (Aldo_ket_red)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46990
PHATRDRAFT_47985

PHATRDRAFT_47959 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47959
PHATRDRAFT_48260 (Peptidase_M16 superfamily)

PHATRDRAFT_47985 - (Peptidase_M16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47985
PHATRDRAFT_48861 erg24_schpo delta-sterol reductase (c-14 sterol reductase) (sterol c14-reductase) (ERG4_ERG24 superfamily)

PHATRDRAFT_48260 - erg24_schpo delta-sterol reductase (c-14 sterol reductase) (sterol c14-reductase) (ERG4_ERG24 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48260
PHATRDRAFT_48869

PHATRDRAFT_48861 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48861
PHATRDRAFT_49743

PHATRDRAFT_48869 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48869
PHATRDRAFT_54420 lumenal-like protein (PsbP superfamily)

PHATRDRAFT_49743 - lumenal-like protein (PsbP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49743
PHATRDRAFT_54920 gtp binding protein (Sar1)

PHATRDRAFT_54420 - gtp binding protein (Sar1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54420

PHATRDRAFT_54920 - phosphoglycerate mutase (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54920
GO ID Go Term p-value q-value Cluster
GO:0019478 D-amino acid catabolism 0.00370462 1 Phatr_bicluster_0095
GO:0015904 tetracycline transport 0.0147418 1 Phatr_bicluster_0095
GO:0006446 regulation of translational initiation 0.0147418 1 Phatr_bicluster_0095
GO:0006352 transcription initiation 0.0436188 1 Phatr_bicluster_0095
GO:0006355 regulation of transcription, DNA-dependent 0.0438421 1 Phatr_bicluster_0095
GO:0006508 proteolysis and peptidolysis 0.0464053 1 Phatr_bicluster_0095
GO:0006520 amino acid metabolism 0.0854566 1 Phatr_bicluster_0095
GO:0006810 transport 0.155631 1 Phatr_bicluster_0095
GO:0008152 metabolism 0.298106 1 Phatr_bicluster_0095
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