scholarly journals A scalable permutation approach reveals replication and preservation patterns of gene coexpression modules

2015 ◽  
Author(s):  
Scott C Ritchie ◽  
Liam G Fearnley ◽  
Gad Abraham ◽  
Michael Inouye
Keyword(s):  
Association Analysis ◽  
Multiple Testing ◽  
Gene Network ◽  
Housekeeping Genes ◽  
Cell Types ◽  
Gene Coexpression ◽  
Muscle Tissues ◽  
Module Preservation ◽  
Network Modules ◽  
Specific Association

Gene coexpression network modules provide a framework for identifying shared biological functions. Analysis of topological preservation of modules across datasets is important for assessing reproducibility, and can reveal common function between tissues, cell types, and species. Although module preservation statistics have been developed, heuristics have been required for significance testing. However, the scale of current and future analyses requires accurate and unbiased p-values, particularly to address the challenge of multiple testing. Here, we developed a rapid and efficient approach (NetRep) for assessing module preservation and show that module preservation statistics are typically non-normal, necessitating a permutation approach. Quantification of module preservation across brain, liver, adipose, and muscle tissues in a BxH mouse cross revealed complex patterns of multi-tissue preservation with 52% of modules showing unambiguous preservation in one or more tissues and 25% showing preservation in all four tissues. Phenotype association analysis uncovered a liver-derived gene module which harboured housekeeping genes and which also displayed adipose and muscle tissue specific association with body weight. Taken together, our study presents a rapid unbiased approach for testing preservation of gene network topology, thus enabling rigorous assessment of potentially conserved function and phenotype association analysis.

INTERACTION OF S PROTEIN/VITRONECTIN WITH CULTURED ENDOTHELIAL CELLS: PROMOTION OF ATTACHMENT AND SPECIFIC BINDING

1987 ◽  
Author(s):  
K T Preissner ◽  
E Anders ◽  
G Müller-Berghaus
Keyword(s):  
Endothelial Cells ◽  
Cell Attachment ◽  
Specific Binding ◽  
Umbilical Vein ◽  
Attachment Site ◽  
Cell Types ◽  
S Protein ◽  
Specific Association ◽  
Umbilical Vein Endothelial Cells ◽  
Adhesive Proteins

The interaction of the complement inhibitor S protein, which is identical to the serum spreading factor, vitronectin, with cultured human endothelial cells of macro- and microvas- cular origin was investigated. Purified S protein, coated for 2 h on polystyrene petri dishes, induced concentration- and time-dependent attachment and spreading of human umbilical vein endothelial cells (HUVEC) as well as human omental tissqe microvasular endothelial cells (HOTMEC) at 37°C. With 3 × 105 cells/ml (final concentration) more than 50% of the cells attached within 2 h incubation at 0.3 - 3 μg/ml S protein. The effect of S protein was specific, since only monospecific antibodies against S protein prevented attachment of cells, while antibodies against fibronectin, fibrinogen or von Wille-brand factor were uneffective. The pentapeptide Gly-Arg-Gly-Asp-Ser, which contains the cell-attachment site of these adhesive proteins including S protein, inhibited the activity of S protein to promote attachment of endothelial cells in a concentration-dependent fashion; at 200 μM peptide, less than 10% of the cells became attached. Direct binding of S protein to HUVEC and HOTMEC was studied with cells in suspension at a concentration of 1 × 106 cells/ml in the presence of 1% (w/v) human serum albumin and 1 mM CaCl2 and was maximal after 120 min. Both cell types bound S protein in a concentration-dependent fashion with an estimated dissociation constant KD=0.2pM. More than 80% of bound radiolabelled S protein was displaced by unlabelled S protein, whereas binding was reduced to about 50% by the addition in excess of either fibronectin, fibrinogen, von Willebrand factor or the pentapeptide. These findings provide evidence for the specific association of S protein with endothelial cells, ultimately leading to attachment and spreading of cells. Although the promotion of attachment was highly specific for S protein, other adhesive proteins than S protein, also known to associate with endothelial cells, may in part compete with direct S protein binding.

scholarly journals Multiple actins in drosophila melanogaster

1979 ◽  
Vol 82 (1) ◽  
pp. 86-92 ◽  
Author(s):  
SJ Horovitch ◽  
RV Storti ◽  
A Rich ◽  
ML Pardue
Keyword(s):  
Body Wall ◽  
Flight Muscle ◽  
Cell Types ◽  
Major Product ◽  
The Other ◽  
Stable Form ◽  
Larval Body ◽  
Drosophila Cell ◽  
Muscle Tissues ◽  
Adult Abdomen

The tissue and developmental specificities of the three Drosophila isoactins, originally identified in primary myogenic cultures and in the permanent Schneider L-2 cell line, have been investigated. Of these three isoactins (I, II, and III), actins I and II are stable and actin III is unstable. Two-dimensional polyacrylamide gel electrophoretic analyses of total cellular extracts after 1-h [(35)S]methionine pulses were performed on a large variety of embryonic, larval, and adult muscle and nonmuscle tissues. The results suggest that isoactins II and III are generalized cellular actins found in all drosophila cell types. Actin I, on the other hand, is muscle-associated and is found exclusively in supercontractile muscle (such as larval body wall and larval and adult viscera) including primary myogenic cell cultures. Although actin I synthesis is not detectable during very early embryogenesis, it is detectable by 25 h and actin I is a major stable actin in all larval muscle tissues. Actin I is synthesized in reduced amounts relative to the other actins in late third instar larvae but is again a major product of actin synthesis in the adult abdomen. A stable actin species with the same pI as actin III has been identified in the adult thorax and appears to be unique to flight muscle tissue. This new stable form of thoracic actin may be the result of a stabilization of the actin III found in other tissues or may be an entirely separate gene product.

microRNA-252 and FoxO repress inflammaging by a dual inhibitory mechanism on Dawdle mediated TGF-β pathway in Drosophila

Genetics ◽  
2021 ◽  
Author(s):  
Xiaofen Wu ◽  
Kongyan Niu ◽  
Xiaofan Wang ◽  
Jing Zhao ◽  
Han Wang ◽  
...  
Keyword(s):  
Cell Types ◽  
Innate Immune ◽  
Low Grade ◽  
Sequencing Analysis ◽  
Immune Genes ◽  
Healthy Longevity ◽  
Muscle Tissues ◽  
Distinct Cell ◽  
A Cell ◽  
Innate Immune Genes

Abstract Inflammaging refers to low-grade, chronically activated innate immunity that has deleterious effects on healthy lifespan. However, little is known about the intrinsic signaling pathway that elicits innate immune genes during aging. Here using Drosophila melanogaster, we profile the microRNA targetomes in young and aged animals, and reveal Dawdle (Daw), an activin-like ligand of the TGF-β pathway, as a physiological target of microRNA-252 (miR-252). We show that miR-252 cooperates with Forkhead box O (FoxO), a conserved transcriptional factor implicated in aging, to repress Daw. Unopposed Daw triggers hyper activation of innate immune genes coupled with a decline in organismal survival. Using adult muscle tissues, single-cell sequencing analysis describes that Daw and its downstream innate immune genes are expressed in distinct cell types, suggesting a cell non-autonomous mode of regulation. We further determine the genetic cascade by which Daw signaling leads to increased Kenny/IKKγ protein, which in turn activates Relish/NF-κB protein and consequentially innate immune genes. Finally, transgenic increase of miR-252 and FoxO pathway factors in wild-type Drosophila extends lifespan and mitigates the induction of innate immune genes in aging. Together, we propose that miR-252 and FoxO promote healthy longevity by cooperative inhibition on Daw mediated inflammaging.

scholarly journals Uncovering co-expression gene network modules regulating fruit acidity in diverse apples

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Yang Bai ◽  
Laura Dougherty ◽  
Lailiang Cheng ◽  
Gan-Yuan Zhong ◽  
Kenong Xu
Keyword(s):  
Gene Network ◽  
Fruit Acidity ◽  
Network Modules

scholarly journals Phage-encoded sigma factors alter bacterial dormancy

2021 ◽  
Author(s):  
Daniel A Schwartz ◽  
Brent K Lehmkuhl ◽  
Jay T Lennon
Keyword(s):  
Bacillus Subtilis ◽  
Metabolic Activity ◽  
Gene Network ◽  
Transcriptional Regulators ◽  
Cell Types ◽  
Sigma Factors ◽  
Lytic Infection ◽  
Parasitic Infections ◽  
Spore Yield

By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to tolerate suboptimal conditions that would otherwise reduce their fitness. Dormancy may also benefit bacteria by serving as a refuge from parasitic infections. Here we focus on dormancy in the Firmicutes, where endospore development is transcriptionally regulated by the expression of sigma factors. A disruption of this process could influence the survivorship and reproduction of phages that infect spore-forming hosts with implications for coevolutionary dynamics. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of sporulation-specific sigma factors were identified in phages that infect spore-forming hosts. Unlike sigma factors required for phage reproduction, the sporulation-like sigma factors were non-essential for lytic infection. However, when expressed in the spore-forming Bacillus subtilis, sigma factors from phages activated the bacterial sporulation gene network and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate a complex and ancient trait in one of the most abundant cell types on Earth.

scholarly journals A Novel Method to Identify the Differences Between Two Single Cell Groups at Single Gene, Gene Pair, and Gene Module Levels

2021 ◽  
Vol 12 ◽  
Author(s):  
Lingyu Cui ◽  
Bo Wang ◽  
Changjing Ren ◽  
Ailan Wang ◽  
Hong An ◽  
...  
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Single Gene ◽  
Cell Types ◽  
Human Pancreas ◽  
Biological Difference ◽  
Cell Clusters ◽  
Cell Groups ◽  
Network Modules ◽  
Differential Gene

Single-cell sequencing technology can not only view the heterogeneity of cells from a molecular perspective, but also discover new cell types. Although there are many effective methods on dropout imputation, cell clustering, and lineage reconstruction based on single cell RNA sequencing (RNA-seq) data, there is no systemic pipeline on how to compare two single cell clusters at the molecular level. In the study, we present a novel pipeline on comparing two single cell clusters, including calling differential gene expression, coexpression network modules, and so on. The pipeline could reveal mechanisms behind the biological difference between cell clusters and cell types, and identify cell type specific molecular mechanisms. We applied the pipeline to two famous single-cell databases, Usoskin from mouse brain and Xin from human pancreas, which contained 622 and 1,600 cells, respectively, both of which were composed of four types of cells. As a result, we identified many significant differential genes, differential gene coexpression and network modules among the cell clusters, which confirmed that different cell clusters might perform different functions.

Developmental expression of Sp1 in the mouse

1991 ◽  
Vol 11 (4) ◽  
pp. 2189-2199
Author(s):  
J D Saffer ◽  
S P Jackson ◽  
M B Annarella
Keyword(s):  
Housekeeping Genes ◽  
Cell Types ◽  
Immunohistochemical Localization ◽  
Developmental Expression ◽  
Regulatory Function ◽  
General Role ◽  
Protein Levels ◽  
Rna Analysis ◽  
Different Cell Types ◽  
Unexpected Difference

The expression of the trans-acting transcription factor Sp1 in mice was defined by a combination of RNA analysis and immunohistochemical localization of the Sp1 protein. Although ubiquitously expressed, there was an unexpected difference of at least 100-fold in the amount of Sp1 message in different cell types. Sp1 protein levels showed corresponding marked differences. Substantial variations in Sp1 expression were also found in some cell types at different stages of development. Sp1 levels appeared to be highest in developing hematopoietic cells, fetal cells, and spermatids, suggesting that an elevated Sp1 level is associated with the differentiation process. These results indicate that Sp1 has a regulatory function in addition to its general role in the transcription of housekeeping genes.

Double-stranded RNA unwinding and modifying activity is detected ubiquitously in primary tissues and cell lines

1990 ◽  
Vol 10 (10) ◽  
pp. 5586-5590
Author(s):  
R W Wagner ◽  
C Yoo ◽  
L Wrabetz ◽  
J Kamholz ◽  
J Buchhalter ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Differentiation ◽  
Cell Lines ◽  
Somatic Cells ◽  
Housekeeping Genes ◽  
Cell Types ◽  
Double Stranded Rna ◽  
Level Of Activity ◽  
Wide Range ◽  
Rna Unwinding

A double-stranded RNA unwinding and modifying activity was found to be present in a wide range of tissues and cell types. The level of activity did not vary significantly with respect to the state of cell differentiation, cell cycle, or transformation. Thus, the unwinding and modifying activity, localized in the nucleus in somatic cells and capable of converting many adenosine residues to inosine, appears to be one of the housekeeping genes.

scholarly journals Attachment of cultured human endothelial cells is promoted by specific association with S protein (vitronectin) as well as with the ternary S protein-thrombin-antithrombin III complex

Blood ◽  
1988 ◽  
Vol 71 (6) ◽  
pp. 1581-1589 ◽  
Author(s):  
KT Preissner ◽  
E Anders ◽  
J Grulich-Henn ◽  
G Muller-Berghaus
Keyword(s):  
Endothelial Cells ◽  
Antithrombin Iii ◽  
Cell Attachment ◽  
Umbilical Vein ◽  
Cell Types ◽  
Human Endothelial Cells ◽  
S Protein ◽  
Major Vessel ◽  
Specific Association ◽  
Dose Dependent

Abstract The interaction of the multifunctional S protein (vitronectin) with cultured human endothelial cells of macrovascular and microvascular origin was investigated. Purified S protein, coated on polystyrene Petri dishes, induced dose-dependent and time-dependent attachment and spreading of human umbilical vein endothelial cells (HUVECs) as well as human omental tissue microvascular endothelial cells (HOTMECs) at 37 degrees C. Not only isolated S protein, but also the ternary S protein- thrombin-antithrombin III (STAT) complex promoted attachment of approximately 90% of the cells within 2 hours at an S protein concentration of 0.13 mumol/L. Inhibition of attachment in these experiments was achieved by the addition of the cell-attachment pentapeptide Gly-Arg-Gly-Asp-Ser and by monospecific antibodies against S protein, whereas nonrelated peptides or antibodies against fibronectin, fibrinogen, or von Willebrand factor (vWF) were ineffective. Direct binding of S protein to HUVECs and HOTMECs was studied with cells in suspension at a density of 1 x 10(6) cells/mL and was maximal after 120 minutes. S protein bound to both cell types in a dose-dependent fashion with an estimated dissociation constant Kd = 0.2 mumol/L. At a 200-fold to 500-fold molar excess of unlabeled S protein, greater than 80% of bound radiolabeled S protein was displaceable, whereas binding was reduced to 30% to 50% by addition of the pentapeptide, the STAT complex, or by physiologic concentrations of fibrinogen or vWF as well as Fab fragments of anti(human S protein)IgG, but not by Fab rabbit IgG. These findings present evidence for the specific association of S protein with endothelial cells ultimately leading to attachment and spreading of cells. Moreover, a novel function for the ternary STAT complex, which induced endothelial cell attachment and spreading virtually identical to free S protein, is described. These data further suggest a possible role for S protein during coagulation as major vessel wall-related adhesive protein at sites of vascular injury.

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