Блог

New!

Coming soon, new totally updated MiROB!
Dear all, we are going to completely reorganize our DB
It will include key new features and improvements:
JS networks instead of Flash
More content, including TF-->miR, LncRNa-->miR and miR-->mRNA interactions
More cancer specific interaction with pathogenic processes: proliferation, invasion, EMT, metastasis, chemoresistance
Disease specific networks with pathogenic processes and cancer hallmarks
Content update every two weeks
You can also leave comments and suggestions for new interaction with yours miRs and genes!

Из каких стран чаще всего делают запросы к MirOB?

Ниже показана статистика по запросам. Один запрос обычно включает несколько генов, на основе которых в результате построили генную сеть.



Удивили мексиканцы. Жаль, не видно откуда пришла 1000 запросов. Но это точно не мои и не из нашей команды.

Самые популярные гены в запросах:
ZEB1 -- в 2779 запросах
TP53 -- в 2428 запросах
ZEB2 -- в 2388 запросах
MIR21 -- в 2241 запросе
MIR145 -- в 1980 запросах
CDH1 -- в 1883 запросах
MIR143 -- в 1833 запросах
MIR155 -- в 1787 запросах
MIR200C -- в 1767 запросах
MIR29A -- в 1748 запросах
KRAS -- в 1747 запросах
MACC1 -- в 1736 запросах
MIR141 -- в 1638 запросах
MIR195 -- в 1558 запросах


С какими продуктами чаще всего используют MirOB

Заглянул на страницу плагина MirOB в отличном проекте BioGPS. Там есть такая графа: "Наиболее часто используется с" (или "С этим продуктом обычно смотрят").

Вот три проекта, которые показываются с MirOB:

Неплохая компания подобралась, но наш продукт будет лучше. Недавно копались в Pathway Commons: визуализации их карт очень трудна для восприятия. Реактом по прежнему хорош, т.к. почти нечем его заменить. WikiPathways, тут получается, что я часто сверяю конкретные сигнальные пути не по их базе, а скорее по базам крупных фармацевтических и биотехнлогических компаний, у них сейчас подобные карты лучше представлены. Хотя, несколько источников всегда лучше одного.

А вот наша страница на omictools показывает следующие проекты, похожие с MirOB:

  • NsRRR — A multivariate regression model capable of using prior biological knowledge expressed as gene...

  • AraPath — A knowledgebase for pathway analysis in Arabidopsis. To create a knowledgebase for plant pathway...

  • Comparison of human cell signaling pathway databases-evolution, drawbacks and challenges — Authors: Chowdhury, S., and Sarkar, R.R. Abstract: Elucidating the complexities of cell...

  • SpliceNet — A method to infer isoform-specific co-expression networks from exon-level RNA-Seq data, using...

  • iPathwayGuide — Allows users to quickly visualize their data through these analyses: gene analysis, gene...

  • Moksiskaan — A computational platform that can be used to integrate information about the connections between...

  • PathwayGuide — It is the most advanced standalone pathway analysis application available. Similar to...

  • PathJam — A public tool which provides an intuitive and user-friendly framework for biological pathway...

  • CellNOpt — A software tool used for creating logic-based models of signal transduction networks using...

  • PathCards — An integrated database of human biological pathways and their annotations. Human pathways were...

  • SignaLink — A signaling pathway resource with multi-layered regulatory networks. Users can effectively...

  • PATHiWAYS — A web tool for the interpretation of the consequences of the combined changes in expression...



Ну как не вспомнить Рея "Наше все" Брэдбери.

Прочитал статью в дайли мейл:
"A Moldovan multi-millionaire whose dream it is to live forever has promised to give $1 million to the first person to reach the age of 123." © dailymail.co.uk

Сразу вспомнил слова классика:

"Знаете, а девяносто лет — это вовсе не так круто, как я думал раньше. И дело не в том, что я езжу по дому в кресле-каталке, застревая на поворотах… Сотня просто звучит солиднее. Представьте себе заголовки во всех газетах мира — «Брэдбери исполнилось сто лет!». Мне сразу выдадут какую-нибудь премию: просто за то, что я ещё не умер." — Рэй Брэдбери



Pathogenetic processes gene networks with microRNA

Today, we have implemented a module showing how to build a network with the pathogenetic processes.



To build the network of pathogenetic processes you must click on "Advanced options", and than click on "only pathogenic processes network" checkbox.



About pathogenetic processes:
Based on the excellent Hanahan and Weinberg Cancer Hallmarks conception, which seems to be the most appropriate for integrative view on cancer, we have created novel cancer-related process ontology - Cancer pathogenic processes (CPP). It comprises various molecular and cellular phenomena that occur in cancer. The major accent of CPP is a specific drug and radiation responses.

Building cancer-specific networks.

Now we made new tool, that allows you to build cancer-specific networks.

Now you can build a network for six major cancers: breast cancer, colorectal cancer, lung cancer, hepatocellular carcinomas, prostate cancer, gastric cancer.

Daily updated with new interactions and updated network

Colorectal cancer example:

Creating cancer type-specific networks

New: Creating cancer type-specific networks (now available for 6 cancers (breast, colorectal, lung, prostate, gastric and HCC hepatocellular carcinoma).

Breast Cancer example:


Shortest interaction paths

We have implemented an advanced algorithm for finding the shortest path between vertices.

In addition to finding the shortest path between two vertices, you can also look for shortcuts that are sure to go through further introduced genes.

And you can specify multiple start and end a few peaks, the algorithm renders all possible ways, if they exist.

We continue to improve the shortest path search algorithms and create something like for example a constructor that flexibly build a complex network of interactions.

MirOB pathway navigator version 0.0017

In the new version (0.0017) of MirOB Pathway Navigator were added following features:
-- the ability to save network as .png file,
-- filters for network visualization: "only microRNA ans transcription factors", "only microRNA", "only transcription factors", "all interactions", "only direct links",
-- filter for reducing the amount of weakly nodes.


In the next series, you will see:
-- the first implementation of the algorithm to find the shortest paths.

MirOB pathway navigator version 0.0016

In the new version (0.0016) of MirOB Pathway Navigator, as an interface, we decided to use the Bootstrap. And as a content management system, we are armed with an latest version of drupal.

Preparation and analysis of data was performed a separate script. Also involved a separate database, which stores the all interactions (a separate back-end part, staffed by our annotators).

also:
-- added diagram of functions (from gene onthology) of network participants
-- the original list of participants displaying individual style
-- fixed a bug introduced by the order of agents

Info

Union Genes (
)
:
Order:

Set 1 unique genes (
)
:
Order:

Set 2 unique genes (
)
:
Order:
Drugs and Targets there..
Oncosupressions microRNA chart there..
Oncogenic microRNA chart there..
graphviz test: