Phatr_bicluster_0090 Residual: 0.41
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_0090 0.41 Phaeodactylum tricornutum
Displaying 1 - 38 of 38
PHATRDRAFT_16445 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT_CobT)

PHATRDRAFT_16445 - nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT_CobT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16445
PHATRDRAFT_19103 30s ribosomal protein s16-like (rpsP)

PHATRDRAFT_19103 - 30s ribosomal protein s16-like (rpsP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19103
PHATRDRAFT_22357 glutaminecatalytic region (COG3968)

PHATRDRAFT_22357 - glutaminecatalytic region (COG3968)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22357
PHATRDRAFT_28684 u4 tri-snrnp-associated 65 kda protein (Peptidase_C19M)

PHATRDRAFT_28684 - u4 tri-snrnp-associated 65 kda protein (Peptidase_C19M)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_28684
PHATRDRAFT_29967 importin-beta n-terminal domain containingexpressed (KAP95)

PHATRDRAFT_29967 - importin-beta n-terminal domain containingexpressed (KAP95)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_29967
PHATRDRAFT_32057 glycerophosphoryl diester phosphodiesterase (PI-PLCc_GDPD_SF superfamily)

PHATRDRAFT_32057 - glycerophosphoryl diester phosphodiesterase (PI-PLCc_GDPD_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32057
PHATRDRAFT_32285 (Ribosomal_L37 superfamily)

PHATRDRAFT_32285 - (Ribosomal_L37 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32285
PHATRDRAFT_33325 ubiquitin conjugating (UBCc superfamily)

PHATRDRAFT_33325 - ubiquitin conjugating (UBCc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33325
PHATRDRAFT_34991

PHATRDRAFT_34991 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34991
PHATRDRAFT_35556 (TPR_MLP1_2)

PHATRDRAFT_35556 - (TPR_MLP1_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35556
PHATRDRAFT_37018 ribosomal protein l29 family protein

PHATRDRAFT_37018 - ribosomal protein l29 family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37018
PHATRDRAFT_40606 (Rav1p_C superfamily)

PHATRDRAFT_40606 - (Rav1p_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40606
PHATRDRAFT_42487

PHATRDRAFT_42487 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42487
PHATRDRAFT_42840 secis binding protein 2 (Ribosomal_L7Ae)

PHATRDRAFT_42840 - secis binding protein 2 (Ribosomal_L7Ae)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42840
PHATRDRAFT_42841 gle1 rna export mediator-like (yeast (GLE1 superfamily)

PHATRDRAFT_42841 - gle1 rna export mediator-like (yeast (GLE1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42841
PHATRDRAFT_42989

PHATRDRAFT_42989 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42989
PHATRDRAFT_43645 type iii effector protein with ppr repeats

PHATRDRAFT_43645 - type iii effector protein with ppr repeats

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43645
PHATRDRAFT_44247 transposase (DDE_3 superfamily)

PHATRDRAFT_44247 - transposase (DDE_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44247
PHATRDRAFT_44762

PHATRDRAFT_44762 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44762
PHATRDRAFT_46248 amp-dependent synthetase and ligase

PHATRDRAFT_46248 - amp-dependent synthetase and ligase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46248
PHATRDRAFT_46708

PHATRDRAFT_46708 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46708
PHATRDRAFT_46880 glutathione s-transferase (Gst)

PHATRDRAFT_46880 - glutathione s-transferase (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46880
PHATRDRAFT_47617 (Lactamase_B superfamily)

PHATRDRAFT_47617 - (Lactamase_B superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47617
PHATRDRAFT_47926

PHATRDRAFT_47926 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47926
PHATRDRAFT_48121

PHATRDRAFT_48121 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48121
PHATRDRAFT_48160 retinoblastoma binding protein 5 (WD40 superfamily)

PHATRDRAFT_48160 - retinoblastoma binding protein 5 (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48160
PHATRDRAFT_48306 translation initiation factorsubunit b (eif-3b) (eIF2A)

PHATRDRAFT_48306 - translation initiation factorsubunit b (eif-3b) (eIF2A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48306
PHATRDRAFT_48388 anthocyanin-related membrane protein 1 (DUF914)

PHATRDRAFT_48388 - anthocyanin-related membrane protein 1 (DUF914)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48388
PHATRDRAFT_48534 trna (nuclear export receptor for trnas)

PHATRDRAFT_48534 - trna (nuclear export receptor for trnas)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48534
PHATRDRAFT_49068 (CRAL_TRIO_2)

PHATRDRAFT_49068 - (CRAL_TRIO_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49068
PHATRDRAFT_49686 tetratricopeptide tpr_2 (TPR)

PHATRDRAFT_49686 - tetratricopeptide tpr_2 (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49686
PHATRDRAFT_49748

PHATRDRAFT_49748 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49748
PHATRDRAFT_49814 (Rav1p_C superfamily)

PHATRDRAFT_49814 - (Rav1p_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49814
PHATRDRAFT_49985 amino acid transporter (Aa_trans superfamily)

PHATRDRAFT_49985 - amino acid transporter (Aa_trans superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49985
PHATRDRAFT_50132 (MIF4G)

PHATRDRAFT_50132 - (MIF4G)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50132
PHATRDRAFT_50295

PHATRDRAFT_50295 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50295
PHATRDRAFT_8230 10 kda (cpn10)

PHATRDRAFT_8230 - 10 kda (cpn10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8230
PHATRDRAFT_9554 30s ribosomal protein s17 (rpsQ)

PHATRDRAFT_9554 - 30s ribosomal protein s17 (rpsQ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9554
GO ID Go Term p-value q-value Cluster
GO:0009236 cobalamin biosynthesis 0.00321067 1 Phatr_bicluster_0090
GO:0006071 glycerol metabolism 0.0127857 1 Phatr_bicluster_0090
GO:0006412 protein biosynthesis 0.0131518 1 Phatr_bicluster_0090
GO:0000059 protein-nucleus import, docking 0.0159584 1 Phatr_bicluster_0090
GO:0006807 nitrogen compound metabolism 0.0440926 1 Phatr_bicluster_0090
GO:0006865 amino acid transport 0.0863845 1 Phatr_bicluster_0090
GO:0006512 ubiquitin cycle 0.115528 1 Phatr_bicluster_0090
GO:0006511 ubiquitin-dependent protein catabolism 0.135415 1 Phatr_bicluster_0090
GO:0006464 protein modification 0.184674 1 Phatr_bicluster_0090
GO:0006457 protein folding 0.317339 1 Phatr_bicluster_0090
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