Phatr_bicluster_0042 Residual: 0.42
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_0042 0.42 Phaeodactylum tricornutum
Displaying 1 - 44 of 44
PHATRDRAFT_10321 26s proteasome regulatory subunit rpn10 (vWFA superfamily)

PHATRDRAFT_10321 - 26s proteasome regulatory subunit rpn10 (vWFA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10321
PHATRDRAFT_10954 bub1 budding uninhibited by benzimidazoles 1 homolog beta (Mad3_BUB1_I superfamily)

PHATRDRAFT_10954 - bub1 budding uninhibited by benzimidazoles 1 homolog beta (Mad3_BUB1_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10954
PHATRDRAFT_11888 nonhistone chromosomal protein 6a (HMGB-UBF_HMG-box)

PHATRDRAFT_11888 - nonhistone chromosomal protein 6a (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11888
PHATRDRAFT_11943 phosphoglycerate mutase (HP_PGM_like)

PHATRDRAFT_11943 - phosphoglycerate mutase (HP_PGM_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11943
PHATRDRAFT_14180 dna repair protein rad54-like (SNF2_N)

PHATRDRAFT_14180 - dna repair protein rad54-like (SNF2_N)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14180
PHATRDRAFT_14212 at4g30600 f17i23_60 (ftsY)

PHATRDRAFT_14212 - at4g30600 f17i23_60 (ftsY)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14212
PHATRDRAFT_17135 cca21_arathcyclin-a2-1 (g2 mitotic-specific cyclin-a2-1)(cyclin-3a) (cyc3a-at) (CYCLIN)

PHATRDRAFT_17135 - cca21_arathcyclin-a2-1 (g2 mitotic-specific cyclin-a2-1)(cyclin-3a) (cyc3a-at) (CYCLIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17135
PHATRDRAFT_23794 calm_pytsp calmodulin (PTZ00184)

PHATRDRAFT_23794 - calm_pytsp calmodulin (PTZ00184)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23794
PHATRDRAFT_25417 gdp-mannose dehydratase (PLN02653)

PHATRDRAFT_25417 - gdp-mannose dehydratase (PLN02653)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25417
PHATRDRAFT_26290 aconitate hydratase 2 (PLN00094)

PHATRDRAFT_26290 - aconitate hydratase 2 (PLN00094)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26290
PHATRDRAFT_26432 dihydrolipoamide dehydrogenase (PRK06327)

PHATRDRAFT_26432 - dihydrolipoamide dehydrogenase (PRK06327)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26432
PHATRDRAFT_26896 histone h4 (H4)

PHATRDRAFT_26896 - histone h4 (H4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26896
PHATRDRAFT_33857

PHATRDRAFT_33857 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33857
PHATRDRAFT_33932

PHATRDRAFT_33932 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33932
PHATRDRAFT_34798 histone h2a (PLN00157)

PHATRDRAFT_34798 - histone h2a (PLN00157)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34798
PHATRDRAFT_36198 at1g78870 f9k20_8 (UBCc)

PHATRDRAFT_36198 - at1g78870 f9k20_8 (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36198
PHATRDRAFT_38865 cyclin d1

PHATRDRAFT_38865 - cyclin d1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38865
PHATRDRAFT_39921 protein kinase (Pkinase)

PHATRDRAFT_39921 - protein kinase (Pkinase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39921
PHATRDRAFT_42547 glycosyl transferase (Gly_transf_sug superfamily)

PHATRDRAFT_42547 - glycosyl transferase (Gly_transf_sug superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42547
PHATRDRAFT_42625 phospholipase a-2-activating protein (WD40 superfamily)

PHATRDRAFT_42625 - phospholipase a-2-activating protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42625
PHATRDRAFT_42672 af492702_2pol protein

PHATRDRAFT_42672 - af492702_2pol protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42672
PHATRDRAFT_43072 tpr repeat

PHATRDRAFT_43072 - tpr repeat

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43072
PHATRDRAFT_43127

PHATRDRAFT_43127 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43127
PHATRDRAFT_43611 ac007060_1 strong similarity to gi (UhpC)

PHATRDRAFT_43611 - ac007060_1 strong similarity to gi (UhpC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43611
PHATRDRAFT_43664 retinoblastoma-associated protein hec (HEC1)

PHATRDRAFT_43664 - retinoblastoma-associated protein hec (HEC1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43664
PHATRDRAFT_44481

PHATRDRAFT_44481 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44481
PHATRDRAFT_45511 t-complex protein 10c isoform 1 (Tcp10_C superfamily)

PHATRDRAFT_45511 - t-complex protein 10c isoform 1 (Tcp10_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45511
PHATRDRAFT_45541

PHATRDRAFT_45541 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45541
PHATRDRAFT_45894 dsh homolog 2

PHATRDRAFT_45894 - dsh homolog 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45894
PHATRDRAFT_46000

PHATRDRAFT_46000 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46000
PHATRDRAFT_46364 fun14 domain containing 2 (FUN14)

PHATRDRAFT_46364 - fun14 domain containing 2 (FUN14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46364
PHATRDRAFT_46913

PHATRDRAFT_46913 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46913
PHATRDRAFT_48463

PHATRDRAFT_48463 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48463
PHATRDRAFT_48923

PHATRDRAFT_48923 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48923
PHATRDRAFT_48960 gamma response i protein

PHATRDRAFT_48960 - gamma response i protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48960
PHATRDRAFT_49083 radiation sensitive protein (Rad52_Rad22)

PHATRDRAFT_49083 - radiation sensitive protein (Rad52_Rad22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49083
PHATRDRAFT_49129

PHATRDRAFT_49129 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49129
PHATRDRAFT_50635 (Alginate_lyase)

PHATRDRAFT_50635 - (Alginate_lyase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50635
PHATRDRAFT_50872 histone protein hist2h3c1 (PTZ00018)

PHATRDRAFT_50872 - histone protein hist2h3c1 (PTZ00018)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50872
PHATRDRAFT_52223 rifk_aspfu riboflavin kinase (flavin mononucleotide kinase 1) (Flavokinase superfamily)

PHATRDRAFT_52223 - rifk_aspfu riboflavin kinase (flavin mononucleotide kinase 1) (Flavokinase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52223
PHATRDRAFT_54355 acetolactatelargebiosynthetic type (IlvB)

PHATRDRAFT_54355 - acetolactatelargebiosynthetic type (IlvB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54355
PHATRDRAFT_54686

PHATRDRAFT_54686 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54686
PHATRDRAFT_7018 at1g60970 t7p1_11 (Clat_adaptor_s superfamily)

PHATRDRAFT_7018 - at1g60970 t7p1_11 (Clat_adaptor_s superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7018
PHATRDRAFT_7359 kinesin motor protein 1-like (Motor_domain superfamily)

PHATRDRAFT_7359 - kinesin motor protein 1-like (Motor_domain superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7359
GO ID Go Term p-value q-value Cluster
GO:0006334 nucleosome assembly 0.0000975 0.224348 Phatr_bicluster_0042
GO:0007001 chromosome organization and biogenesis (sensu Eukaryota) 0.000117881 0.271245 Phatr_bicluster_0042
GO:0000074 regulation of cell cycle 0.0168296 1 Phatr_bicluster_0042
GO:0006614 SRP-dependent cotranslational protein-membrane targeting 0.029302 1 Phatr_bicluster_0042
GO:0006099 tricarboxylic acid cycle 0.0464863 1 Phatr_bicluster_0042
GO:0007018 microtubule-based movement 0.16389 1 Phatr_bicluster_0042
GO:0006281 DNA repair 0.18369 1 Phatr_bicluster_0042
GO:0006310 DNA recombination 0.198245 1 Phatr_bicluster_0042
GO:0006512 ubiquitin cycle 0.203042 1 Phatr_bicluster_0042
GO:0009058 biosynthesis 0.235853 1 Phatr_bicluster_0042
Log in to post comments