ONCO.IO gene regulatory networks analysis in cancer and microRNA

Total number of interactions:
17886

binding of miRNA:
6521

transcription regulation:
4820

drug interactions:
454

chemo/drugresistance:
211

metabolic reactions:
8244

TF => ncRNA reactions:
750

drug => gene/miR reactions:
454

Path. processes associations:
15568

Diseases associations:
9863

Pubmeds:
19743

Express.levels associations:
4154

Prognosis associations:
1954

Diagnosis associations:
52

Biomarker localization:
5300

Cell lines associations:
18658

Tumor stage associations:
55

Methods associations:
52200

Cell Localization:
413

number of new added interactions:
for last week:
209
(
-19
)
for last 2 weeks:
437

for last month:
919 (
+456
)

for last two month:
1382

graph view

top annotators of last month:
rhizoman1:
919
(
+456
)

Processes

Pathogenic process (PP) - molecular, cellular or tissue malfunction determining initiation, development and outcome of disease. Full list of PP is here
Interactions (or edges) are associated with pathogenic process and can influence as positively and negatively on the process.

Processes:

Genes and ncRNAs

Symbol:

Citations:

[2020, Journal of Allergy and Clinical Immunology] IL-32γ suppressed atopic dermatitis through inhibition of miR-205 expression via inactivation of nuclear factor-kappa B -- "The miRNA-gene network of miR-205 and RELA (p65) were analyzed by using the ONCO.IO database tool (https://onco.io), which is based on the manually curated annotation of experimentally verified molecular interactions described in the literature."
[2019, Tarbiat Modares University, Modares Journal of Biotechnology] Data Mining as a Tool to Identify miRNAs which Regulate Stemness, Metastasis and Drug Resistance in Gastric Cancer -- " ONCO.IO database and KEGG pathway have been done to obtain the interaction between miRNA-miRNA target and cancer-related signaling pathway respectively."
[2018, MDPI, Cancers] Epigenetic Regulation by lncRNAs: An Overview Focused on UCA1 in Colorectal Cancer -- "We confirmed the UCA1/miRNA-regulated genes in these pathways with the miRNA network analysis tool ONCO.IO (Figure 2). Figure 2. The regulation by Urothelial Cancer Associated 1 (UCA1)-associated miRNAs. All 29 miRNAs published to interact with UCA1 (Table 4) were submitted to the miRNA network analysis tool ONCO.IO and the downstream-regulated genes are visualized (https://onco.io/main.php). All 29 miRNAs published to interact with UCA1 in diverse cancer cell types (Table 4) were submitted to the miRNA network analysis tool ONCO.IO and their interaction with chemoresistance-related genes were visualized (Receptors: TGFBR2, NOTCH1, FGFR1;"
[2018, biorxiv.org] Comparative Proteogenomic Analysis of Right-sided Colon Cancer, Left-sided Colon Cancer and Rectal Cancers Reveal Distinct Mutational Profiles -- "Further network analysis was carried out using a newer version, ONCO.IO (https://onco.io), of the MicroRNA OncoBase (MirOB) web tool (http://mirob.interactome.ru/)."
LabWorm ONCO.IO profile

Previous version of the ONCO.IO tool (https://mirob.interactome.ru)

[PLOS | ONE 2017] Meta-analysis of miRNA expression profiles for prostate cancer recurrence following radical prostatectomy -- "Network-based analysis was performed using a MIROB web tool (http://mirob.interactome.ru/) which has been designed to support analysis of microRNA expression data. MIROB (microRNA OncoBase) scans the set of input miRNAs to build any cancer pathways, detects key targets and Transcription Factors (TF) of candidate miRNAs, identifies any possible correlation between key targets and TF of candidate miRNAs and other diseases, and makes pathogenesis network. ... MIROB tool was used to perform regulatory microRNA network analysis to identify regulators responsible for the observed patterns in miRNA meta-analysis studies. ... To understand the association of the DE microRNAs list with the most significant target genes and transcription factors, we conducted a regulatory gene network analysis using the MIROB web tool. CDKN1A and LASP1 were amongst the most significant target genes associated with the DE microRNAs."
[Placenta 2017] Dysregulated placental microRNAs in Early and Late onset Preeclampsia -- "RNA target prediction for selected miRNAs was performed with TargetScan v.7.0 [20], DIANA tools [[21], [22], [23]] and the miROB annotation web tool (http://mirob.interactome.ru/)."
[PLOS | one] Proteasome Functioning in Breast Cancer: Connection with Clinical-Pathological Factors. Elena E. Shashova, Yulia V. Lyupina, Svetlana A. Glushchenko, Elena M. Slonimskaya, Olga V. Savenkova, Alexey M. Kulikov "Regulatory network between ERα and proteasome immune subunit LMP2 in breast cancer. MIR, microRNA; SOX4, PU.1 (SPI 1), MYC, transcription factors. Created within open informatics site MirOB"
[Uppsala: Acta Universitatis Upsaliensis, 2014 / .pdf] Small Intestinal Neuroendocrine Tumor Analyses. Somatostatin Analog Effects and MicroRNA Profiling. Su-Chen Li /UPPSALA UNIVERSITET "MicroRNA OncoBase (MirOB) (www.mirob.interactome.ru/) software was used to identify biologically relevant gene networks and any potential miRNA target gene’s ontology information."
[Tumor Biology, jan 2015/springer] Over-expression of miR-10b in NPC patients: correlation with LMP1 and Twist1 -- "Supplementary Fig. S2: Regulatory network of miR-10b. This schematic representation is created within the open informatic’s site MirOB "
Targeted cancer therapy based on blocking the expression of genes and small doses of oxaliplatin. (file [.pdf])
[innoros.ru] Searching and analysis novel gene targets for colorectal cancer therapy by multiple comparison of clinical OMICs data and detail bioinformatics analysis, including network and pathway approaches, created by Stas Poyarkov and Russians leading bioinformatics team.
[researchgate.net] Does anyone have experience with Multi-Omics Interaction Network (GE + miRNA + Methylation + CNA)?
[.pdf] [Диссертация] "Профилирование экспрессии микроРНК в опухолях молочной железы и шеи. Сравнительный анализ". Веряскина Юлия Андреевна. (2016 год). "Экспериментально доказанные гены-мишени миРНК и транскрипционные факторы. Массив данных сформирован при помощи базы данных mirOB (http://mirob.interactome.ru)."
[www.sys-med.de] Network analysis of HDAC-controlled microRNAs in neuroblastoma -- "Predicted protein-coding mRNA targets will be then systematically mapped to cellular pathways from the KEGG database and the mirOB database for cancer-specific pathways involving microRNAs among other database resources."
Медицинская Генетика, 2015 г., Том 14, №3 (153). Материалы VII Съезда Российского общества медицинских генетиков. -- "Анализ с помощью интерактивной базы для раково-специфичных генных сетей mirOB показал различные патогенетические пути, в которые вовлечены микроРНК разных групп. МикроРНК с положительными корреляциями связаны с процессами эпителиально-мезенхимального перехода (EMT), клеточным циклом и пролиферацией; смешанная группа связана с миграцией, инвазией и апоптозом."
Omictools MirOB profile
MirOB plugin in BioGPS

News:

Moscow Cancer Center Employees Threaten to Quit as Doctor Resignation Wave Hits Capital 03 October 2019 16:50:10 by Sasha Fokin
Doctors from the Research Institute of Pediatric Oncology and Hematology of the Blokhin National Medical Research Center for Oncology demanded a change of leadership. In a statement on the Doctors Alliance’s YouTube channel, they said they would quit otherwise.

Doctors complained of poor conditions for patients: lack of ventilation and mold in crowded rooms. Management, they said, instead of economic issues is engaged in "hardware struggle."

Another reason for writing applications was the dismissal of Georgy Mentkevich, the creator of the country's first bone marrow transplant department. Other specialists were forced to quit along with him.

At least 26 childrens oncologists at the Blokhin Cancer Center have threatened to quit if its recently appointed leader isnt fired, pay transparency isnt introduced and overcrowded and mold-covered wards arent replaced.

Thanks to our visitors! 26 July 2019 16:25:13 by Sasha Fokin
We thank the anonymous guest for pointing out the vulnerabilities. They are was patched, but there is still much to be done, and we are gradually completing it. While the project is running in the background.

miRs in prostate cancer: comlex regulatory connections with cancer hallmarks 18 January 2019 23:53:17 by Rhizoman1
Next week we will annotate regulatory interactions in prostate cancer. Prostate cancer (PCa) is considered the most prevalent malignancy and the second major cause of cancer-related death in males from Western countries. Androgen deprivation therapy (ADT) is the primary treatment option for male patients with advanced symptomatic PCa. Castration-resistant prostate cancer (CRPC) refers to the continuous progression of PCa following ADT. We will focus on the role of non-coding RNAs and transcription factors in prostate cancer development and progression.

Paywall: The Business of Scholarship 26 December 2018 16:17:32 by Sasha Fokin
Paywall: The Business of Scholarship is a documentary which focuses on the need for open access to research and science, questions the rationale behind the $25.2 billion a year that flows into for-profit academic publishers, examines the 35-40% profit margin associated with the top academic publisher Elsevier and looks at how that profit margin is often greater than some of the most profitable tech companies like Apple, Facebook and Google.

Paywall: The Business of Scholarship (Full Movie) CC BY 4.0 from Paywall The Movie on Vimeo.

The program of reduce the critical dependence of Russian science on foreign genetic and biological databases. 26 December 2018 16:10:04 by Sasha Fokin
"The Ministry of Education and Science proposes to allocate 220.5 billion rubles. on the development of genetic technologies in the framework of the federal scientific and technical program for the years 2019-2027. This is stated in the draft government decree on the approval of the program, published on Friday on the federal portal of draft regulations. The implementation of the program is designed to "reduce the critical dependence of Russian science on foreign genetic and biological data bases, foreign specialized software and devices, the programs passport says. In Russia, bioinformatics and genetic databases, basic reagents and software products and equipment prototypes should be created." The leading scientific organization will be the Kurchatov Institute. The ONCO.IO is made entirely by our forces and means without the help of any other structures and organizations. This is a completely independent product. For all inhabitants of the planet Earth, we provide equal access to ONCO.IO and his services.

Immune response interactome! 06 October 2018 01:24:29 by Rhizoman1
T-cell-DC, signaling and regulatory pathways that develop immune response. Co-regulatory and repressor molecules. Receptors, signaling molecules, transcription factors as are drivers of anti-cancer immunity. Next week we will annotate immunoregulatory interactome! This is dedicated to the Nobel prize in Physiology or Medicine 2018!

Hooray! Today our database reached the milestone of 15,000 manualy curated validated links 27 September 2018 15:33:44 by Sasha Fokin

Blog

Last saved networks:

Angiogenesis_signaling [30 June 2020 16:06:20 by guest ]
Angiogenesis_signaling [30 June 2020 15:54:39 by guest ]
MAPK_JNK_signaling [29 June 2020 19:47:17 by guest ]
COVID-19_severe_signature_genes [29 June 2020 18:13:05 by guest ]
Apoptosis_common [29 June 2020 17:28:08 by guest ]
MAPK_JNK_signaling [29 June 2020 13:29:05 by guest ]
MAPK_p38_signaling [28 June 2020 14:04:49 by guest ]
MAPK_p38_signaling [28 June 2020 02:18:32 by guest ]
MAPK_p38_signaling [28 June 2020 02:14:12 by guest ]
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Telomerase [28 June 2020 01:18:21 by guest ]
AKT_signaling [28 June 2020 01:03:48 by guest ]
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MAPK_ERK1/2_signaling [25 June 2020 16:02:38 by guest ]
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ADAM [24 June 2020 03:51:10 by guest ]
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The Fanconi Anemia Pathway in Cancer [22 June 2020 14:16:45 by guest ]
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Apoptosis_common [22 June 2020 00:22:45 by guest ]
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Response to Hypoxia [21 June 2020 17:01:05 by guest ]
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Response to Hypoxia [21 June 2020 02:07:15 by guest ]
Response to Hypoxia [20 June 2020 18:21:16 by guest ]
USP7 [19 June 2020 16:06:33 by guest ]
USP7 [19 June 2020 16:01:47 by guest ]
Inflammasome activation and regulation [18 June 2020 19:10:12 by guest ]

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ONCO.IO

Long non-coding RNA interactions page

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