Organism : Methanococcus maripaludis S2 | Module List :
MMP0719

transcriptional regluator

CircVis
Functional Annotations (3)
Function System
Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0719
(Mouseover regulator name to see its description)

MMP0719 is regulated by 8 influences and regulates 5 modules.
Regulators for MMP0719 (8)
Regulator Module Operator
MMP0041
MMP1275
35 combiner
MMP0637
MMP1015
35 combiner
MMP0637
MMP1376
35 combiner
MMP1275
MMP1376
35 combiner
H2 43 ef
MMP0052
MMP0097
43 combiner
MMP0097
MMP1100
43 combiner
MMP0168
MMP1100
43 combiner

Warning: MMP0719 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
731 6.90e-04 ACcgcTaAATCGtTTTTaAAAT
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732 1.60e+00 ACTAacttaaTAAATatg.CTTT
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747 0.00e+00 Ttg.agGgGGg
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748 2.80e+01 ACCCCtTctCAtatActCccG
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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 MMP0719

MMP0719 is enriched for 3 functions in 3 categories.
Module neighborhood information for MMP0719

MMP0719 has total of 57 gene neighbors in modules 35, 43
Gene neighbors (57)
Gene Common Name Description Module membership
Antisense_10 None 2, 43, 150
MMP0076 deoxyribonuclease 24, 35
MMP0077 radical SAM domain-containing protein 35, 104
MMP0102 pcm protein-L-isoaspartate O-methyltransferase 2, 43, 150
MMP0172 hypothetical protein MMP0172 9, 43
MMP0219 ppaC putative manganese-dependent inorganic pyrophosphatase 35, 126
MMP0294 Pyrrolo-quinoline quinone 43, 125
MMP0304 N-glycosylase/DNA lyase 22, 33, 43, 152
MMP0305 2-oxoacid ferredoxin oxidoreductase subunit beta 2, 33, 43
MMP0306 oxidoreductase family protein member subunit alpha 2, 33, 43
MMP0383 slp S-layer protein 35, 126
MMP0590 glycosyl transferase family protein 35, 86
MMP0591 hypothetical protein MMP0591 35, 126
MMP0592 hypothetical protein MMP0592 35, 126
MMP0593 walker type ATPase 35, 126
MMP0614 iron-sulfur flavoprotein 43, 125, 151
MMP0634 hypothetical protein MMP0634 43, 108
MMP0710 HAD superfamily ATPase 43, 159
MMP0711 corA magnesium/cobalt transporter CorA 43, 108
MMP0718 hypothetical protein MMP0718 35, 43
MMP0719 transcriptional regluator 35, 43
MMP0762 hypothetical protein MMP0762 19, 43
MMP0763 hypothetical protein MMP0763 43, 123
MMP0783 hypothetical protein MMP0783 43, 160
MMP0784 hypothetical protein MMP0784 43, 163
MMP0964 hypothetical protein MMP0964 43, 108
MMP0996 hypothetical protein MMP0996 43, 90, 125
MMP0997 blue (type1) copper domain-containing protein 23, 43, 90, 125
MMP1073 ehbC putative monovalent cation/H+ antiporter subunit G 35, 106
MMP1190 FKBP-type peptidylprolyl isomerase 35, 107
MMP1191 mch N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase 35, 126
MMP1257 NERD domain-containing protein 19, 43
MMP1291 glycoside hydrolase family protein 43, 166
MMP1292 glycoside hydrolase 15-like protein 43, 166
MMP1293 group 1 glycosyl transferase 43, 159
MMP1294 glgA starch synthase 43, 150, 166
MMP1295 glucose-6-phosphate isomerase 43, 75
MMP1373 purP 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase 14, 35
MMP1493 hypothetical protein MMP1493 35, 58
MMP1518 sulfate/molybdate ABC-transporter ATPase subunit 35, 126
MMP1519 anion transport system permease 35, 126
MMP1520 hydrogenase accessory protein HypB 35, 126
MMP1560 mtrE tetrahydromethanopterin S-methyltransferase subunit E 35, 126
MMP1561 mtrD tetrahydromethanopterin S-methyltransferase subunit D 35, 126
MMP1562 mtrC tetrahydromethanopterin S-methyltransferase subunit C 35, 126
MMP1563 mtrB tetrahydromethanopterin S-methyltransferase subunit B 35, 126
MMP1564 mtrA tetrahydromethanopterin S-methyltransferase subunit A 35, 126
MMP1565 or900 tetrahydromethanopterin S-methyltransferase subunit A 35, 126
MMP1566 mtrG tetrahydromethanopterin S-methyltransferase subunit G 35, 126
MMP1567 mtrH tetrahydromethanopterin S-methyltransferase subunit H 35, 126
MMP1604 hypothetical protein MMP1604 43, 166
MMP1643 hypothetical protein MMP1643 35, 38
MMP1644 hypothetical protein MMP1644 35, 126
MMP1703 hypothetical protein MMP1703 43, 108
MMP1717 type 12 methyltransferase 35, 126
MMP1718 hypothetical protein MMP1718 35, 126
Unanno_57 None 43, 124
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 MMP0719
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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