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Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells

ABSTRACT: A systems biology approach in which qualitative modeling based on combining boolean networks and in silico perturbation experiments were employed to identify 15 pluripotency regulating cytokines or cytokine related genes. IL-11 was validated as a novel factor capable of maintaing the undifferentiated state of human embryonic stem cells in the absence of exogenously added bFGF to the culture acting via a different mechanims than bFGF.

ORGANISM(S): Homo sapiens

PROVIDER: GSE51159 | GEO | 2013/09/26

SECONDARY ACCESSION(S): PRJNA221368

REPOSITORIES: GEO

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Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells

Project description:A systems biology approach in which qualitative modeling based on combining boolean networks and in silico perturbation experiments were employed to identify 15 pluripotency regulating cytokines or cytokine related genes. IL-11 was validated as a novel factor capable of maintaing the undifferentiated state of human embryonic stem cells in the absence of exogenously added bFGF to the culture acting via a different mechanims than bFGF. Transcriptomic microarray data of eight overexpression and knock-down experiments were used for qualitative modeling based on boolean networks to predict novel factors - mainly cytokines - that maintain pluripotent human embryonic stem cells in the absence of bFGF in culture. The culture was maintained for at least 9 passages using and stained positive for alcaline phosphatase staining, OCT3/4, SOX2, NANOG, TRA1-60. Microarray based gene expression profiling showed that the IL-11 treatment occupies an intermediate state, between bFGF treatment and the negative control which is no cytokine treatment as judged by hierarchical clustering. Moreover, KEGG pathway analysis indicates common and additional distinct mechanisms of bFGF and IL-11 dependant pluripotency dependant mechanisms.

2013-09-26 | E-GEOD-51159 | biostudies-arrayexpress

Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells.

Project description: Not available

| S-EPMC3809568 | biostudies-literature

MSI2 is required for maintaining activated myelodysplastic syndrome stem cells

2016-02-16 | GSE76840 | GEO

MSI2 is required for maintaining activated myelodysplastic syndrome stem cells

Project description:Analysis of musashi2 contribution towards maintaing myelodysplastic phenotype in stem cells. We find that musashi2 plays an integral role in maintaining the myelodysplastic phenotype Control, NUP98-HOXD13; NHD13, NHD13/MSI2 bone marrow was transplated allowed to engraft into lethally irradiated congenic CD45.1 animals. Mice were then fed doxycycline to induce MSI2 overexpression. Mice were induced for 3 months and then CD45.2 Lineage lo Sca1+ and Kit+ cells were sorted and then assessed for gene expression.

2016-02-16 | E-GEOD-76840 | biostudies-arrayexpress

A robust qualitative transcriptional signature for the early diagnosis of gastric cancer

Project description:Pathological examination of gastroscopy biopsy specimens will make false diagnosis for gastric cancer (GC) due to inaccurate sampling locations and/or insufficient sampling amount. We extracted a robust qualitative transcriptional signature, based on the within-sample relative expression orderings (REOs) of gene pairs, to discriminate both GC tissues and adjacent-normal tissues from non-GC gastritis and normal gastric tissues.The qualitative transcriptional signature can be robustly applied at the individual level to aid the diagnosis of early GC.

2018-07-10 | GSE116782 | GEO

Plant Boolean Implication Network

Project description:Numerous gene expression datasets from diverse plant tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available plant datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

2018-08-29 | GSE119083 | GEO

Human Boolean Implication Network

Project description:Numerous gene expression datasets from diverse human tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available human datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

2018-08-29 | GSE119087 | GEO

Mouse Boolean Implication Network

Project description:Numerous gene expression datasets from diverse mouse tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available mouse datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

2018-08-29 | GSE119085 | GEO

Fly Boolean Implication Network

Project description:Numerous gene expression datasets from diverse fly tissue samples have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available fly datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated.

2018-08-29 | GSE119084 | GEO

A Qualitative Transcriptional Signature for the Histological Classification of Non-Small Cell Lung Cancer

Project description:Histological classification by routine pathology assessment with hematoxylin-eosin staining and immunostaining for poorly differentiated tumors, particularly those from small biopsies, is still challenging. In this study, using gene expression profiles of pathologically-determined lung squamous cell carcinomas and adenocarcinomas, denoted as pSCC and pADC respectively, we developed a qualitative transcriptional signature, based on the within-sample relative gene expression orderings (REOs) of gene pairs, to individually distinguish ADC from SCC. The signature was validated in the frozen tissues, FFPE materials, mixed tumors, small biopsy specimens and poorly differentiated samples.In summary, the qualitative signature, independent of the subjective diagnosis of pathologists, would be an effective auxiliary tool in distinguishing ADC from SCC.

2018-10-11 | GSE121090 | GEO

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