Organism : Methanococcus maripaludis S2 | Module List :
MMP0257 tbp

transcription factor

CircVis
Functional Annotations (7)
Function System
TATA-box binding protein (TBP), component of TFIID and TFIIIB cog/ cog
DNA binding go/ molecular_function
RNA polymerase II transcription factor activity go/ molecular_function
transcription factor TFIID complex go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription initiation from RNA polymerase II promoter go/ biological_process
Basal transcription factors kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0257
(Mouseover regulator name to see its description)

MMP0257 is regulated by 9 influences and regulates 33 modules.
Regulators for MMP0257 tbp (9)
Regulator Module Operator
MMP0031
MMP1646
28 combiner
MMP1052 28 tf
MMP1052
MMP1137
28 combiner
MMP1100
MMP1442
28 combiner
MMP1100
MMP1646
28 combiner
MMP0168 58 tf
MMP0629
MMP1015
58 combiner
MMP0907 58 tf
MMP1015 58 tf

Warning: MMP0257 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
717 2.80e-04 Aaat.GGtGa
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718 2.30e+01 cgGgaGTTcG
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777 3.90e-01 accTaCAaaaatAca.tatAt
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778 1.20e+03 CGTTTCCTCGTGCAC
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Motif Help

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.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for MMP0257

MMP0257 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
TATA-box binding protein (TBP), component of TFIID and TFIIIB cog/ cog
DNA binding go/ molecular_function
RNA polymerase II transcription factor activity go/ molecular_function
transcription factor TFIID complex go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription initiation from RNA polymerase II promoter go/ biological_process
Basal transcription factors kegg/ kegg pathway
Module neighborhood information for MMP0257

MMP0257 has total of 60 gene neighbors in modules 28, 58
Gene neighbors (60)
Gene Common Name Description Module membership
Antisense_3 None 58, 70
Antisense_8 None 28, 153
MMP0050 ribH 6,7-dimethyl-8-ribityllumazine synthase 58, 98
MMP0051 hisE phosphoribosyl-ATP pyrophosphatase 58, 98
MMP0059 hypothetical protein MMP0059 8, 58, 64
MMP0072 hypothetical protein MMP0072 28, 129
MMP0096 putative GntR family transcriptional regulator 39, 58
MMP0097 transcriptional regulator 58, 166
MMP0165 ABC transporter 28, 115
MMP0166 MATE family drug/sodium antiporter 1, 28
MMP0167 ABC transporter ATP-binding protein 1, 28
MMP0168 ParR family transcriptional regulator 1, 28
MMP0180 ribC riboflavin synthase 1, 58
MMP0181 hypothetical protein MMP0181 4, 58
MMP0209 hypothetical protein MMP0209 30, 58
MMP0210 hypothetical protein MMP0210 58, 140
MMP0256 hisH imidazole glycerol phosphate synthase subunit HisH 28, 58
MMP0257 tbp transcription factor 28, 58
MMP0265 hypothetical protein MMP0265 28, 129
MMP0313 hypothetical protein MMP0313 28, 73
MMP0342 hypothetical protein MMP0342 28, 98
MMP0369 hypothetical protein MMP0369 58, 151
MMP0480 hypothetical protein MMP0480 58, 99
MMP0487 hypothetical protein MMP0487 58, 98
MMP0499 hypothetical protein MMP0499 22, 28, 144, 146, 153
MMP0511 fmdB molybdenum containing formylmethanofuran dehydrogenase subunit B 5, 28
MMP0524 hypothetical protein MMP0524 4, 58, 146, 153, 163
MMP0536 hypothetical protein MMP0536 1, 28
MMP0608 2-hydroxyglutaryl-CoA dehydratase subunit A-like protein 1, 28
MMP0613 acetolactate decarboxylase 58, 124
MMP0630 feoB ferrous iron transporter 28, 76, 106, 121
MMP0631 putative iron dependent repressor 28, 121, 144
MMP0684 hsp20 heat shock protein Hsp20 28, 121
MMP0712 amino acid ABC transporter substrate-binding protein 58, 154
MMP0722 hypothetical protein MMP0722 58, 160
MMP0734 hypothetical protein MMP0734 30, 58, 154
MMP0757 hypothetical protein MMP0757 58, 146
MMP0788 hypothetical protein MMP0788 58, 117
MMP0812 hypothetical protein MMP0812 12, 28
MMP0843 hypothetical protein MMP0843 22, 28
MMP0922 putative phage infection protein 58, 98
MMP0923 dapB dihydrodipicolinate reductase 58, 98
MMP0932 MCP methylation inhibitor CheC 58, 59, 98
MMP1051 surE stationary phase survival protein SurE 12, 28, 106
MMP1066 putative molybdenum cofactor biosynthesis protein MoaC 28, 133
MMP1134 type A flavoprotein 58, 123
MMP1135 flavodoxin:beta-lactamase-like 58, 123
MMP1136 rubrerythrin 58, 123
MMP1171 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase 28, 66
MMP1229 FUN14 family protein 58, 123
MMP1265 glutamyl-tRNA(Gln) amidotransferase subunit E 28, 129
MMP1303 sensory transduction histidine kinase 4, 28, 66
MMP1439 cofactor-independent phosphoglycerate mutase 58, 123
MMP1467 ehaT hypothetical protein MMP1467 28, 129, 133
MMP1493 hypothetical protein MMP1493 35, 58
MMP1550 NADP oxidoreductase, coenzyme F420-dependent 1, 58
MMP1573 bioD dethiobiotin synthase 28, 106
MMP1657 hypothetical protein MMP1657 21, 28
Unanno_47 None 58, 99
Unanno_59 None 28, 104, 133
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for MMP0257
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend