Organism : Methanococcus maripaludis S2 | Module List :
MMP0041 tfb

transcription initiation factor IIB

CircVis
Functional Annotations (8)
Function System
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
protein binding go/ molecular_function
transcription factor complex go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
Basal transcription factors kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0041
(Mouseover regulator name to see its description)

MMP0041 is regulated by 11 influences and regulates 6 modules.
Regulators for MMP0041 tfb (11)
Regulator Module Operator
MMP0018
MMP0480
160 combiner
MMP0097
Formate
160 combiner
MMP0097
MMP1015
160 combiner
MMP0097
MMP1376
160 combiner
MMP0257
MMP1712
160 combiner
MMP0480 160 tf
MMP0480
MMP0719
160 combiner
MMP0018
MMP1100
19 combiner
MMP0052
Formate
19 combiner
MMP0097
Formate
19 combiner
MMP1100 19 tf

Warning: MMP0041 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
699 7.40e+01 TaTaTaaa.tTTtctAtTtga.tt
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700 1.10e+04 GCCGGA
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967 8.70e-01 ATgTcgGGtaT
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968 3.20e+02 cAgGgag.aGG
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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 MMP0041

MMP0041 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
protein binding go/ molecular_function
transcription factor complex go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
Basal transcription factors kegg/ kegg pathway
Module neighborhood information for MMP0041

MMP0041 has total of 53 gene neighbors in modules 19, 160
Gene neighbors (53)
Gene Common Name Description Module membership
Antisense_27 None 19, 50
MMP0038 type II secretion system protein 115, 160
MMP0039 hypothetical protein MMP0039 115, 160
MMP0040 type II secretion system protein E 115, 160
MMP0041 tfb transcription initiation factor IIB 19, 160
MMP0042 H/ACA RNA-protein complex component Gar1 19, 108
MMP0086 tfx putative transcriptional regulator 150, 160
MMP0234 hypothetical protein MMP0234 46, 160
MMP0235 hypothetical protein MMP0235 75, 160
MMP0237 hypothetical protein MMP0237 75, 160
MMP0238 hypothetical protein MMP0238 160, 166
MMP0240 hypothetical protein MMP0240 75, 160
MMP0278 putative CBS domain-containing signal transduction protein 19, 90
MMP0299 hypothetical protein MMP0299 154, 160
MMP0344 hypothetical protein MMP0344 19, 90
MMP0405 gch3 GTP cyclohydrolase III 19, 92
MMP0407 hypothetical protein MMP0407 8, 19, 89
MMP0452 hypothetical protein MMP0452 75, 160
MMP0458 hypothetical protein MMP0458 75, 160
MMP0595 hypothetical protein MMP0595 75, 160
MMP0632 ATP/GTP-binding motif-containing protein 19, 115
MMP0636 hypothetical protein MMP0636 75, 160
MMP0656 hypothetical protein MMP0656 46, 160
MMP0721 ferredoxin 125, 160
MMP0722 hypothetical protein MMP0722 58, 160
MMP0723 hypothetical protein MMP0723 75, 160
MMP0736 PRC-barrel domain-containing protein 8, 19, 38
MMP0762 hypothetical protein MMP0762 19, 43
MMP0783 hypothetical protein MMP0783 43, 160
MMP1067 succinate dehydrogenase/fumarate reductase iron-sulfur subunit 19, 123
MMP1223 hypothetical protein MMP1223 19, 123
MMP1244 fwdH tungsten containing formylmethanofuran dehydrogenase subunit H 19, 89
MMP1245 fwdF tungsten containing formylmethanofuran dehydrogenase subunit F 19, 89
MMP1246 fwdG tungsten containing formylmethanofuran dehydrogenase subunit G 19, 89
MMP1247 fwdD tungsten containing formylmethanofuran dehydrogenase subunit D 19, 89
MMP1248 fwdA tungsten containing formylmethanofuran dehydrogenase subunit A 19, 89
MMP1249 fwdC tungsten containing formylmethanofuran dehydrogenase subunit C 19, 89
MMP1257 NERD domain-containing protein 19, 43
MMP1258 hemB delta-aminolevulinic acid dehydratase 19, 124
MMP1279 camphor resistance protein CrcB 115, 160
MMP1475 hypothetical protein MMP1475 19, 50
MMP1511 amino acid carrier protein 19, 92
MMP1555 mcrB methyl-coenzyme M reductase I subunit beta 19, 89
MMP1556 mcrD methyl-coenzyme M reductase I, protein D 19, 89
MMP1557 mcrC methyl coenzyme M reductase I, protein C 19, 89
MMP1558 mcrG methyl-coenzyme M reductase I subunit gamma 19, 89
MMP1559 mcrA methyl-coenzyme M reductase I subunit alpha 19, 89
MMP1586 hypothetical protein MMP1586 19, 100
MMP1608 hypothetical protein MMP1608 150, 160
MMP1609 ftr formylmethanofuran--tetrahydromethanopterin formyltransferase 19, 89
MMP1610 hypothetical protein MMP1610 19, 139
MMP1637 hypothetical protein MMP1637 13, 19
MMP1712 LysR family transcriptional regulator 19, 106
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 MMP0041
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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