Organism : Methanococcus maripaludis S2 | Module List :
MMP1137

Lrp/AsnC family transcriptional regulator

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1137
(Mouseover regulator name to see its description)

MMP1137 is regulated by 11 influences and regulates 6 modules.
Regulators for MMP1137 (11)
Regulator Module Operator
MMP0031
H2
78 combiner
MMP0033 78 tf
MMP0052
MMP1304
78 combiner
MMP0465
Formate
78 combiner
MMP0840
H2
78 combiner
MMP1052 78 tf
MMP1304 78 tf
MMP1704 78 tf
MMP0033
H2
70 combiner
MMP0465
Formate
70 combiner
MMP0568
H2
70 combiner

Warning: MMP1137 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
801 1.50e+02 AGAtATgt.gT.gtaAaAACA
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802 4.00e+03 cCgGtaaAAAAgTtTCCgAA
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817 1.30e+00 GTTTT.A.CaGCac
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818 9.50e+02 gtATAacgtaTA.aTataGGTagg
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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 MMP1137

MMP1137 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
iron ion binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for MMP1137

MMP1137 has total of 57 gene neighbors in modules 70, 78
Gene neighbors (57)
Gene Common Name Description Module membership
Antisense_3 None 58, 70
MMP0183 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 8, 70
MMP0220 Sodium/proline symporter-related 70, 140
MMP0270 Fe-S cluster domain-containing protein 21, 70
MMP0272 ABC transporter ATPase 21, 70
MMP0273 comA phosphosulfolactate synthase 21, 70
MMP0274 hypE hydrogenase expression/formation protein HypE 67, 70
MMP0290 nac nascent polypeptide-associated complex protein 8, 78
MMP0308 SirA family protein 7, 78
MMP0309 DsrE family protein 8, 78
MMP0345 hypothetical protein MMP0345 7, 70
MMP0355 hypothetical protein MMP0355 52, 78
MMP0359 glycosyl transferase family protein 7, 78
MMP0371 hypothetical protein MMP0371 8, 70
MMP0377 isoleucyl-tRNA synthetase-like protein 52, 78
MMP0381 3-isopropylmalate dehydratase small subunit 78, 80
MMP0382 putative ATPase RIL 8, 70, 78
MMP0385 pyrH uridylate kinase 70, 78
MMP0391 aspC aspartate aminotransferase 77, 78
MMP0396 eno phosphopyruvate hydratase 77, 78
MMP0397 alaS alanyl-tRNA synthetase 70, 78
MMP0398 hypothetical protein MMP0398 70, 80, 87
MMP0399 htpX heat shock protein HtpX 70, 78
MMP0400 ehbQ amino acid-binding ACT domain-containing protein 70, 78
MMP0402 hypothetical protein MMP0402 15, 70
MMP0410 prsA ribose-phosphate pyrophosphokinase 52, 78
MMP0448 hypothetical protein MMP0448 4, 70
MMP0449 ferredoxin 13, 70
MMP0450 ferredoxin 1, 70
MMP0451 hypothetical protein MMP0451 1, 70
MMP0498 hypothetical protein MMP0498 52, 70
MMP0500 Iron-sulfur flavoprotein-like protein 70, 78
MMP0618 hypothetical protein MMP0618 21, 70
MMP0619 hypothetical protein MMP0619 21, 70
MMP0620 atwA methyl coenzyme M reductase, component A2 21, 70
MMP0704 ParA type ATPase 8, 78, 112
MMP0816 seryl-tRNA synthetase-like protein 8, 70
MMP0898 cellulose-binding protein 8, 70
MMP0899 ATP/GTP-binding motif-containing protein 70, 81
MMP0900 rhodanese domain-containing protein 70, 81
MMP0904 selD selenophosphate synthetase 21, 70
MMP0949 tRNA CCA-pyrophosphorylase 4, 70
MMP0954 hypothetical protein MMP0954 21, 70
MMP0966 cobA uroporphyrin-III C-methyltransferase 68, 70
MMP1022 hypothetical protein MMP1022 21, 70
MMP1023 TetR family transcriptional regulator 8, 21, 78
MMP1089 polysaccharide biosynthesis protein 14, 70
MMP1093 coaD phosphopantetheine adenylyltransferase 52, 70
MMP1116 cellulase 40, 78
MMP1129 ppiB cyclophilin type peptidyl-prolyl cis-trans isomerase 40, 70, 78
MMP1137 Lrp/AsnC family transcriptional regulator 70, 78
MMP1138 thiM hydroxyethylthiazole kinase 70, 78
MMP1139 thiE thiamine-phosphate pyrophosphorylase 27, 70, 78
MMP1352 ribulose-1,5-biphosphate synthetase 7, 8, 78
MMP1589 carA carbamoyl phosphate synthase small subunit 7, 78
Unanno_33 None 52, 78
Unanno_8 None 8, 78
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 MMP1137
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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