- 13 putative driver genes were identified from TCGA somatic mutation data including TP53, CTNNB1, and AXIN1. Some genes were associated with clinical characteristics and survival outcomes.
- Multi-omic data from TCGA including RNA-seq, miRNA-seq, DNA methylation, and copy number variation were integrated using similarity network fusion and clustering. This identified 5 subtypes of HCC with different survival profiles.
- Predictive models were built for each subtype on individual omics datasets, showing concordance between 56-87%. Analysis of gene expression profiles revealed different active biological processes between the subtypes.
Assessing the clinical utility of cancer genomic and proteomic data across tu...Gul Muneer
Molecular profiling of tumors promises to advance the clinical
management of cancer, but the benefits of integrating
molecular data with traditional clinical variables have not been
systematically studied. Here we retrospectively predict patient
survival using diverse molecular data (somatic copy-number
alteration, DNA methylation and mRNA, microRNA and protein
expression) from 953 samples of four cancer types from The
Cancer Genome Atlas project. We find that incorporating
molecular data with clinical variables yields statistically
significantly improved predictions (FDR < 0.05) for three
cancers but those quantitative gains were limited (2.2–23.9%).
Additional analyses revealed little predictive power across
tumor types except for one case. In clinically relevant genes,
we identified 10,281 somatic alterations across 12 cancer types
in 2,928 of 3,277 patients (89.4%), many of which would
not be revealed in single-tumor analyses. Our study provides
a starting point and resources, including an open-access
model evaluation platform, for building reliable prognostic and
therapeutic strategies that incorporate molecular data
Presentation by Scott Woodman, MD, PhD. Presented at the 2018 Eyes on a Cure: Patient & Caregiver Symposium, hosted by the Melanoma Research Foundation's CURE OM initiative.
Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neu...Gul Muneer
Systemic cross-talk between lung tumors and bones
Bone marrow–derived myeloid cells can accumulate within tumors and foster
cancer outgrowth. Local immune-neoplastic interactions have been intensively
investigated, but the contribution of the systemic host environment to tumor growth
remains poorly understood. Here, we show in mice and cancer patients (n = 70) that
lung adenocarcinomas increase bone stromal activity in the absence of bone
metastasis. Animal studies reveal that the cancer-induced bone phenotype involves
bone-resident osteocalcin-expressing (Ocn+) osteoblastic cells. These cells promote
cancer by remotely supplying a distinct subset of tumor-infiltrating SiglecFhigh
neutrophils, which exhibit cancer-promoting properties. Experimentally reducing
Ocn+ cell numbers suppresses the neutrophil response and lung tumor outgrowth.
These observations posit osteoblasts as remote regulators of lung cancer and
identify SiglecFhigh neutrophils as myeloid cell effectors of the osteoblast-driven
protumoral response
Nanodroplet processing platform for deep and quantitative proteome profiling ...Gul Muneer
Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.
Assessing the clinical utility of cancer genomic and proteomic data across tu...Gul Muneer
Molecular profiling of tumors promises to advance the clinical
management of cancer, but the benefits of integrating
molecular data with traditional clinical variables have not been
systematically studied. Here we retrospectively predict patient
survival using diverse molecular data (somatic copy-number
alteration, DNA methylation and mRNA, microRNA and protein
expression) from 953 samples of four cancer types from The
Cancer Genome Atlas project. We find that incorporating
molecular data with clinical variables yields statistically
significantly improved predictions (FDR < 0.05) for three
cancers but those quantitative gains were limited (2.2–23.9%).
Additional analyses revealed little predictive power across
tumor types except for one case. In clinically relevant genes,
we identified 10,281 somatic alterations across 12 cancer types
in 2,928 of 3,277 patients (89.4%), many of which would
not be revealed in single-tumor analyses. Our study provides
a starting point and resources, including an open-access
model evaluation platform, for building reliable prognostic and
therapeutic strategies that incorporate molecular data
Presentation by Scott Woodman, MD, PhD. Presented at the 2018 Eyes on a Cure: Patient & Caregiver Symposium, hosted by the Melanoma Research Foundation's CURE OM initiative.
Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neu...Gul Muneer
Systemic cross-talk between lung tumors and bones
Bone marrow–derived myeloid cells can accumulate within tumors and foster
cancer outgrowth. Local immune-neoplastic interactions have been intensively
investigated, but the contribution of the systemic host environment to tumor growth
remains poorly understood. Here, we show in mice and cancer patients (n = 70) that
lung adenocarcinomas increase bone stromal activity in the absence of bone
metastasis. Animal studies reveal that the cancer-induced bone phenotype involves
bone-resident osteocalcin-expressing (Ocn+) osteoblastic cells. These cells promote
cancer by remotely supplying a distinct subset of tumor-infiltrating SiglecFhigh
neutrophils, which exhibit cancer-promoting properties. Experimentally reducing
Ocn+ cell numbers suppresses the neutrophil response and lung tumor outgrowth.
These observations posit osteoblasts as remote regulators of lung cancer and
identify SiglecFhigh neutrophils as myeloid cell effectors of the osteoblast-driven
protumoral response
Nanodroplet processing platform for deep and quantitative proteome profiling ...Gul Muneer
Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of ~1500 to ~3000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of ~2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.
The use of genetic engineering technology in animals has been associated with ethical issues, some of which relate to animal welfare. Discuss examples of genetically engineering animals and evaluate the ethical concerns of genetic engineering.
As an uncommon malignant tumor, hypopharyngeal cancer accounts for 3–5% of head and neck tumors [1]. Most pathological types of hypopharyngeal cancer are squamous cell carcinoma. Due to the occult anatomical location of hypopharyngeal cancer and poor surgical effect, local recurrence or distant metastasis often occurs in patients with hypopharyngeal cancer following surgery.
An Evolutionary and Structural Analysis of the Connective Tissue Growth Facto...Ashley Kennedy
The connective tissue growth factor (CTGF) gene is known to be important in cell growth, bone and cartilage differentiation, and wound healing. The molecular mechanisms and exact role that CTGF plays in these processes are still unclear. A greater understanding of the evolutionary history of this gene may help identify regions of the gene important at the molecular level of wound healing. Aligning CTGF sequences from 19 different species allowed for identification of regions in the CTGF gene that are conserved across evolutionary history. We have matched single nucleotide polymorphisms (SNPs) detected by sequencing individuals at Plymouth State to these highly conserved regions. Surprisingly, we have identified 18 SNPs in humans within regions of the gene that are highly conserved. In addition, an excess of SNPs that cause amino acid changes in these regions suggests there is positive selective pressure on this gene in humans. Using a comparative protein modeling utility, RaptorX, we have identified SNPs that have significant impact on the protein structure of CTGF. Understanding evolutionary pressures on CTGF and identifying significantly different variants among humans can help increase understanding of this gene and its involvement in healing.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
Conference talk at BioSB 2015 in Lunteren, The Netherlands
* Date: 20 May 2015
* Title: "Integrative network based analysis of mRNA and miRNA expression in vitamin D3-treated cancer cells"
The use of genetic engineering technology in animals has been associated with ethical issues, some of which relate to animal welfare. Discuss examples of genetically engineering animals and evaluate the ethical concerns of genetic engineering.
As an uncommon malignant tumor, hypopharyngeal cancer accounts for 3–5% of head and neck tumors [1]. Most pathological types of hypopharyngeal cancer are squamous cell carcinoma. Due to the occult anatomical location of hypopharyngeal cancer and poor surgical effect, local recurrence or distant metastasis often occurs in patients with hypopharyngeal cancer following surgery.
An Evolutionary and Structural Analysis of the Connective Tissue Growth Facto...Ashley Kennedy
The connective tissue growth factor (CTGF) gene is known to be important in cell growth, bone and cartilage differentiation, and wound healing. The molecular mechanisms and exact role that CTGF plays in these processes are still unclear. A greater understanding of the evolutionary history of this gene may help identify regions of the gene important at the molecular level of wound healing. Aligning CTGF sequences from 19 different species allowed for identification of regions in the CTGF gene that are conserved across evolutionary history. We have matched single nucleotide polymorphisms (SNPs) detected by sequencing individuals at Plymouth State to these highly conserved regions. Surprisingly, we have identified 18 SNPs in humans within regions of the gene that are highly conserved. In addition, an excess of SNPs that cause amino acid changes in these regions suggests there is positive selective pressure on this gene in humans. Using a comparative protein modeling utility, RaptorX, we have identified SNPs that have significant impact on the protein structure of CTGF. Understanding evolutionary pressures on CTGF and identifying significantly different variants among humans can help increase understanding of this gene and its involvement in healing.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
A normal cell can be transformed into a cancerous cell. Discuss the therapeutic strategies that are employed to target the cellular transformation process for cancer prevention and treatment.
Conference talk at BioSB 2015 in Lunteren, The Netherlands
* Date: 20 May 2015
* Title: "Integrative network based analysis of mRNA and miRNA expression in vitamin D3-treated cancer cells"
Developing a framework for for detection of low frequency somatic genetic alt...Ronak Shah
Cancer is a complex, heterogeneous disease of the genome. Most cancers result
from an accumulation of multiple genetic alterations that lead to dysfunction of cancer-associated
genes and pathways. Recent advances in sequencing technology have enabled comprehensive
profiling of genetic alterations in cancer. We have established a targeted sequencing platform
(IMPACT: Integrated Mutation Profiling of Actionable Cancer Targets) using hybridization capture and
next-generation sequencing (NGS) technology, which can reveal mutations, indels and copy number
alterations involving 340 cancer related genes.
Proteogenomic analysis of human colon cancer reveals new therapeutic opportun...Gul Muneer
We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.
Identification, annotation and visualisation of extreme changes in splicing w...Mar Gonzàlez-Porta
Talk for the ECCB'14 workshop: Analysis of differential isoform usage by RNA-seq: statistical methodologies and open software - Strasbourg, 7th September 2014
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...QIAGEN
Pancreatic cancer is a uniquely lethal malignancy characterized by frequent mutations in KRAS, CDKN2A, SMAD4, TP53 and many others. We have shown that KRAS mutation can be detected in cell-free, circulating tumor DNA (ctDNA) isolated from the plasma in a subset of patients and is associated with poor prognosis. The ability to simultaneously detect multiple pancreatic cancer-specific mutations in ctDNA would open a new avenue for detection of clinically-relevant mutations. In this study, we performed ultra-deep sequencing of ctDNA from advanced pancreatic cancer patients prior to treatment with Gemcitabine and Erlotinib following target enrichment. Somatic, non-synonymous variants were identified in 29 different genes at allele frequencies typically less than 0.5%. Updated results of ultra-deep NGS analysis will be presented.
Comprehensive molecular characterization of gastric adenocarcinoma
The Cancer Genome Atlas Research Network ( TCGA)
Nature, July 2014
JC, by
Mohsin Maqbool, AIIMS
Visual Exploration of Clinical and Genomic Data for Patient StratificationNils Gehlenborg
Talk presented at the Simons Foundation Biotech Symposium "Complex Data Visualization: Approach and Application" (12 September 2014)
http://www.simonsfoundation.org/event/complex-data-visualization-approach-and-application/
In this talk I describe how we integrated a sophisticated computational framework directly into the StratomeX visualization technique to enable rapid exploration of tens of thousands of stratifications in cancer genomics data, creating a unique and powerful tool for the identification and characterization of tumor subtypes. The tool can handle a wide range of genomic and clinical data types for cohorts with hundreds of patients. StratomeX also provides direct access to comprehensive data sets generated by The Cancer Genome Atlas Firehose analysis pipeline.
http://stratomex.caleydo.org
BERT: Bidirectional Encoder Representations from TransformersLiangqun Lu
BERT was developed by Google AI Language and came out Oct. 2018. It has achieved the best performance in many NLP tasks. So if you are interested in NLP, studying BERT is a good way to go.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
আমাদের সবার জন্য খুব খুব গুরুত্বপূর্ণ একটি বই ..বিসিএস, ব্যাংক, ইউনিভার্সিটি ভর্তি ও যে কোন প্রতিযোগিতা মূলক পরীক্ষার জন্য এর খুব ইম্পরট্যান্ট একটি বিষয় ...তাছাড়া বাংলাদেশের সাম্প্রতিক যে কোন ডাটা বা তথ্য এই বইতে পাবেন ...
তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
বিসিএস ও ব্যাংক এর লিখিত পরীক্ষা ...+এছাড়া মাধ্যমিক ও উচ্চমাধ্যমিকের স্টুডেন্টদের জন্য অনেক কাজে আসবে ...
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
it describes the bony anatomy including the femoral head , acetabulum, labrum . also discusses the capsule , ligaments . muscle that act on the hip joint and the range of motion are outlined. factors affecting hip joint stability and weight transmission through the joint are summarized.
The simplified electron and muon model, Oscillating Spacetime: The Foundation...RitikBhardwaj56
Discover the Simplified Electron and Muon Model: A New Wave-Based Approach to Understanding Particles delves into a groundbreaking theory that presents electrons and muons as rotating soliton waves within oscillating spacetime. Geared towards students, researchers, and science buffs, this book breaks down complex ideas into simple explanations. It covers topics such as electron waves, temporal dynamics, and the implications of this model on particle physics. With clear illustrations and easy-to-follow explanations, readers will gain a new outlook on the universe's fundamental nature.
Delivering Micro-Credentials in Technical and Vocational Education and TrainingAG2 Design
Explore how micro-credentials are transforming Technical and Vocational Education and Training (TVET) with this comprehensive slide deck. Discover what micro-credentials are, their importance in TVET, the advantages they offer, and the insights from industry experts. Additionally, learn about the top software applications available for creating and managing micro-credentials. This presentation also includes valuable resources and a discussion on the future of these specialised certifications.
For more detailed information on delivering micro-credentials in TVET, visit this https://tvettrainer.com/delivering-micro-credentials-in-tvet/
A review of the growth of the Israel Genealogy Research Association Database Collection for the last 12 months. Our collection is now passed the 3 million mark and still growing. See which archives have contributed the most. See the different types of records we have, and which years have had records added. You can also see what we have for the future.
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
How to Build a Module in Odoo 17 Using the Scaffold MethodCeline George
Odoo provides an option for creating a module by using a single line command. By using this command the user can make a whole structure of a module. It is very easy for a beginner to make a module. There is no need to make each file manually. This slide will show how to create a module using the scaffold method.
Thinking of getting a dog? Be aware that breeds like Pit Bulls, Rottweilers, and German Shepherds can be loyal and dangerous. Proper training and socialization are crucial to preventing aggressive behaviors. Ensure safety by understanding their needs and always supervising interactions. Stay safe, and enjoy your furry friends!
1. Multi-omic data integration to
stratify population in hepatocellular
carcinoma (HCC)
Masters Defense presented by Liangqun Lu
Molecular Biosciences & Bioengineering
Committee:
Dr. Lana Garmire (Chair)
Dr. Maarit Tiirikainen
Dr. Herbert Yu
2. Hepatocellular carcinoma (HCC)
•Liver cancer is the 6th
common cancer worldwide
•Liver cancer being 2nd leading cause of cancer death globally
•HCC accounting for approximately 80% liver cancer cases
•Five-year survival rate: 17%
•According to statistical reports from World Health Organization:
• Estimation of new cases: 782,500 (554,400 males and 228,100 females)
•Estimation of deaths: 745,500 (521,000 males and 224,500 females)
4. Somatic alteration studies on HCC
* WGS: whole genome sequencing, WES: whole exome sequencing
Study Group Technique Sample size Candidate onco-event
Li et al.(M. Li et al., 2011) China WES 10 ARID2 (inactivation)
Guichard(Guichard et al., 2012) France WES 24 ARID1A, RPS6KA3, NFE2L2,
IRF2 (new)
J. Huang et al.(J. Huang et al., 2012) China WES 110 ARID1A
Cleary et al.(Cleary et al., 2013) US WES 87 MLL
Totoki et al.(Totoki et al., 2011) Japan WGS 10 TSC1 (nonsense substitution)
Fujimoto et al.(Fujimoto et al., 2012) Japan WGS 27 ARID1A, ARID1B, ARID2,
KMT2A, MLL3
Kan et al.(Kan et al., 2013) US WGS 88 Wnt pathway, JAK/STAT pathway
Ahn et al.(Ahn et al., 2014) Korea WES 231 TP53, CTNNB1, AXIN1,
RPS6KA3, RB1
Schulze et al.(Schulze et al., 2015) France WES 243 CTNNB1; TP53; AXIN1
5. Somatically altered pathways
Cell cycle
Wnt signaling
Oxidative stress
Epigenetic and chromatin remodeling
AKT-mTOR-MAPK signaling
Telomere maintenance
HCC progression and somatic alterations, from the Hepatocellular carcinoma Nature Reviews Disease Primers
(Llovet et al., 2016).
6. Research goal / specific aims
•Specific aim 1: Clinical and transcriptomics associations of putative
driver mutations in hepatocellular carcinoma
•Specific aim 2: Integrating multi-omic data sets to determine
subtypes and build predictive models of new patients
•Our goal in this study is to associate the somatic mutations with
clinical characteristics and gene expression, and build molecular
classification from multi-omic data integration on HCC samples.
7. TCGA Samples
•TCGA Liver hepatocellular carcinoma (LIHC) data
Data types Platforms Samples
Exome-sequencing Illumina Genome Analyzer DNA Sequencing 198 (T)
198 (N)
Copy-number Variation Affymetrix Genome-Wide Human SNP Array 6.0 371 (T)
83 (N)
RNA-seq Illumina HiSeq 2000 RNA Sequencing Version 2
analysis
371 (T)
50 (N)
DNA Methylation Illumina Infinium Human DNA Methylation 450 377 (T)
50 (N)
miRNA-seq Illumina HiSeq 2000 miRNA Sequencing 372 (T)
51 (N)
Clinical Age, Gender, Race, Stage, Grade and Risks 377 cases
* T: tumor samples; N: normal samples (solid tissue)
8. Aim 1 – Clinical and transcriptomics associations of
putative driver mutations in hepatocellular carcinoma
•Cancer is initiated and developed due to the accumulation of somatic
genomic alterations through the widespread impact on gene products
and phenotypic properties.
•Although significantly mutated genes have been identified in a series of
cohort studies in liver cancer, the association with gene expression and
clinical characteristics has not been investigated.
•Data sets: Exome-seq; RNA-seq and miRNA-seq
12. Results
•Detection of putative driver genes
• Mutation point
• Significance and Frequency
• Lollipop plot of point mutation
•Associations among clinical characteristics and putative driver genes
•Associations between mRNA transcriptome and putative driver gene
mutations
• Gene count
• Pathway Enrichment
•The associations between miRNA expression and putative driver gene
mutations
13. Figure 1. Putative driver genes in TCGA HCC cohort and their KEGG pathways
20. Summary
•From TCGA somatic mutation data, we selected 13 putative driver
genes and did a systematic analysis on mutation points, mutation
frequency and pathways.
•In the association with clinical characteristics and survival, we showed
that these putative driver genes are related to clinical features, and the
multiple genes demonstrating prediction on survival.
•In the association with gene expression, we showed that some genes
regulate some pathways in common, which might explain the mutation
exclusivity.
21. Aim 2 – Multi-omic data integration to stratify
population in hepatocellular carcinoma
•Population stratification helps guide precise targeted therapeutics
•No comprehensive data integration considering complementary
information from different omic data has been investigated to build
classification on HCC.
•Data sets: RNA-seq, miRNA-seq, DNA methylation and copy number
variation from TCGA
23. Data integration(SNF) and Clustering (Spectral Clustering)
Similarity Network Fusion from (B. Wang et al., 2014)
Spectral Clustering
From online slideshare
24. Results
•Integrative clustering of HCC multi-omic data
• Unsupervised clustering on integrative data
• Different number of clusters
• Association with survival
•SNF subtypes associated with clinical characteristics
• Survival curves
•SNF subtypes associated with putative driver genes
•SNF subtype predictive model on each dataset
•SNF subtype feature on gene expression profiling
30. Figure 6. active genes and active pathways in subtypes from gene expression level
31. Summary
•Through the four omic-data integration, we optimized five subtypes
based on survival association.
•We built predictive models on each omic dataset and the
concordance between one omic data and fused subtypes ranges
56-87%.
•The subtypes have different active biological processes at
transcriptional level.