Phatr_bicluster_0019 Residual: 0.43
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_0019 0.43 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_10508 af436836_1 at5g35180 t25c13_60 (DUF1336 superfamily)

PHATRDRAFT_10508 - af436836_1 at5g35180 t25c13_60 (DUF1336 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10508
PHATRDRAFT_10704 cyclin dependent kinase c (STKc_CDK9_like)

PHATRDRAFT_10704 - cyclin dependent kinase c (STKc_CDK9_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10704
PHATRDRAFT_11414 mitochondrial phosphate carrier protein (Mito_carr)

PHATRDRAFT_11414 - mitochondrial phosphate carrier protein (Mito_carr)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11414
PHATRDRAFT_13192 cdc5 cell division cycle 5-like (SANT)

PHATRDRAFT_13192 - cdc5 cell division cycle 5-like (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13192
PHATRDRAFT_14090 nuclear accommodation of mitochondria (AAA_11)

PHATRDRAFT_14090 - nuclear accommodation of mitochondria (AAA_11)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14090
PHATRDRAFT_14771 interferon-induced mx protein (DLP_1)

PHATRDRAFT_14771 - interferon-induced mx protein (DLP_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14771
PHATRDRAFT_14983 dead box atp-dependent rna helicase (DEADc)

PHATRDRAFT_14983 - dead box atp-dependent rna helicase (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14983
PHATRDRAFT_15217 d-isomer specific 2-hydroxyacidnad-binding (2-Hacid_dh_C superfamily)

PHATRDRAFT_15217 - d-isomer specific 2-hydroxyacidnad-binding (2-Hacid_dh_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15217
PHATRDRAFT_21988 (PRK09279)

PHATRDRAFT_21988 - (PRK09279)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21988
PHATRDRAFT_22404 pyruvate kinase (PRK06247)

PHATRDRAFT_22404 - pyruvate kinase (PRK06247)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22404
PHATRDRAFT_31364 trna-dihydrouridine synthase (DUS_like_FMN)

PHATRDRAFT_31364 - trna-dihydrouridine synthase (DUS_like_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31364
PHATRDRAFT_33458 (Trp-synth-beta_II superfamily)

PHATRDRAFT_33458 - (Trp-synth-beta_II superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33458
PHATRDRAFT_33638

PHATRDRAFT_33638 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33638
PHATRDRAFT_37853

PHATRDRAFT_37853 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37853
PHATRDRAFT_38120 (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_38120 - (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38120
PHATRDRAFT_38270 3-5 exonuclease (DnaQ_like_exo superfamily)

PHATRDRAFT_38270 - 3-5 exonuclease (DnaQ_like_exo superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38270
PHATRDRAFT_38995

PHATRDRAFT_38995 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38995
PHATRDRAFT_39832 glycogenin-like protein (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_39832 - glycogenin-like protein (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39832
PHATRDRAFT_40300

PHATRDRAFT_40300 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40300
PHATRDRAFT_40694

PHATRDRAFT_40694 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40694
PHATRDRAFT_44124

PHATRDRAFT_44124 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44124
PHATRDRAFT_45758 (CysJ)

PHATRDRAFT_45758 - (CysJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45758
PHATRDRAFT_46160 protein phosphatase (PP2Cc)

PHATRDRAFT_46160 - protein phosphatase (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46160
PHATRDRAFT_47020 cytokine induced apoptosis inhibitorisoform cra_b (CIAPIN1)

PHATRDRAFT_47020 - cytokine induced apoptosis inhibitorisoform cra_b (CIAPIN1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47020
PHATRDRAFT_48732 prolyl 4-hydroxylase alpha subunit (2OG-FeII_Oxy_3 superfamily)

PHATRDRAFT_48732 - prolyl 4-hydroxylase alpha subunit (2OG-FeII_Oxy_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48732
PHATRDRAFT_48931

PHATRDRAFT_48931 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48931
PHATRDRAFT_49205 jun d proto-oncogene (B_zip1)

PHATRDRAFT_49205 - jun d proto-oncogene (B_zip1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49205
PHATRDRAFT_49461

PHATRDRAFT_49461 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49461
PHATRDRAFT_50015

PHATRDRAFT_50015 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50015
GO ID Go Term p-value q-value Cluster
GO:0016051 carbohydrate biosynthesis 0.00886476 1 Phatr_bicluster_0019
GO:0016310 phosphorylation 0.0307218 1 Phatr_bicluster_0019
GO:0006470 protein amino acid dephosphorylation 0.0414888 1 Phatr_bicluster_0019
GO:0006096 glycolysis 0.0752324 1 Phatr_bicluster_0019
GO:0019538 protein metabolism 0.0773059 1 Phatr_bicluster_0019
GO:0006468 protein amino acid phosphorylation 0.323667 1 Phatr_bicluster_0019
GO:0006810 transport 0.352949 1 Phatr_bicluster_0019
GO:0006355 regulation of transcription, DNA-dependent 0.394049 1 Phatr_bicluster_0019
GO:0006118 electron transport 0.408154 1 Phatr_bicluster_0019
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