Categorical data analysis in experimental biology.

Abstract:

:The categorical data set is an important data class in experimental biology and contains data separable into several mutually exclusive categories. Unlike measurement of a continuous variable, categorical data cannot be analyzed with methods such as the Student's t-test. Thus, these data require a different method of analysis to aid in interpretation. In this article, we will review issues related to categorical data, such as how to plot them in a graph, how to integrate results from different experiments, how to calculate the error bar/region, and how to perform significance tests. In addition, we illustrate analysis of categorical data using experimental results from developmental biology and virology studies.

journal_name

Dev Biol

journal_title

Developmental biology

authors

Xu B,Feng X,Burdine RD

doi

10.1016/j.ydbio.2010.08.018

subject

Has Abstract

pub_date

2010-12-01 00:00:00

pages

3-11

issue

1

eissn

0012-1606

issn

1095-564X

pii

S0012-1606(10)01016-X

journal_volume

348

pub_type

杂志文章,评审
  • Plasticity in the nervous system of adult hydra. I. The position-dependent expression of FMRFamide-like immunoreactivity.

    abstract::The plasticity of nerve cells expressing the neuropeptide FMRFamide was examined in adult hydra. Using a whole-mount technique with indirect immunofluorescence, the spatial pattern of neurons showing FMRFamide-like immunoreactivity (FLI) was visualized. These neurons were located in the tentacles, hypostome, and pedun...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/0012-1606(86)90142-9

    authors: Koizumi O,Bode HR

    更新日期:1986-08-01 00:00:00

  • Distinct roles for retinoic acid receptors alpha and beta in early lung morphogenesis.

    abstract::Retinoic acid (RA) signaling is required for normal development of multiple organs. However, little is known about how RA influences the initial stages of lung development. Here, we used a combination of genetic, pharmacological and explant culture approaches to address this issue, and to investigate how signaling by ...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2005.10.045

    authors: Desai TJ,Chen F,Lü J,Qian J,Niederreither K,Dollé P,Chambon P,Cardoso WV

    更新日期:2006-03-01 00:00:00

  • Specificity of gene action during central nervous system development in Drosophila melanogaster: analysis of the lethal (1) optic ganglion reduced locus.

    abstract::A newly defined genetic locus designated lethal (1) optic ganglion reduced (l(1)ogre: 1-18.8, 6E1/2-6E4/5) is characterized. Four alleles have been isolated, one organismal viable and three organismal lethals. Histological analyses of these mutants at the light microscopic level have detected defects only in the devel...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/0012-1606(85)90009-0

    authors: Lipshitz HD,Kankel DR

    更新日期:1985-03-01 00:00:00

  • Activin signaling functions upstream of Gbb to regulate synaptic growth at the Drosophila neuromuscular junction.

    abstract::Activins are members of the TGF-ss superfamily of secreted growth factors that control a diverse array of processes in vertebrates including endocrine function, cell proliferation, differentiation, immune response and wound repair. In Drosophila, the Activin ligand Dawdle (Daw) has been shown to regulate several aspec...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2010.03.012

    authors: Ellis JE,Parker L,Cho J,Arora K

    更新日期:2010-06-15 00:00:00

  • ZYG-1 promotes limited centriole amplification in the C. elegans seam lineage.

    abstract::Genome stability relies notably on the integrity of centrosomes and on the mitotic spindle they organize. Structural and numerical centrosome aberrations are frequently observed in human cancer, and there is increasing evidence that centrosome amplification can promote tumorigenesis. Here, we use C. elegans seam cells...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2018.01.001

    authors: Wolf B,Balestra FR,Spahr A,Gönczy P

    更新日期:2018-02-15 00:00:00

  • Coordinate regulation of the expression of axonal proteins by the axonal microenvironment.

    abstract::The axonal functions that act in the formation of the neuronal network have been shown to occur in close interdependence with the tissue that surrounds the growing axons. However, little is known about the molecular building blocks underlying axonal functions, although more than 400 axonal proteins have been identifie...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/0012-1606(86)90090-4

    authors: Sonderegger P,Lemkin PF,Lipkin LE,Nelson PG

    更新日期:1986-11-01 00:00:00

  • Laser ablation of the sonic hedgehog-a-expressing cells during fin regeneration affects ray branching morphogenesis.

    abstract::The zebrafish fin is an excellent system to study the mechanisms of dermal bone patterning. Fin rays are segmented structures that form successive bifurcations both during ontogenesis and regeneration. Previous studies showed that sonic hedgehog (shha) may regulate regenerative bone patterning based on its expression ...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2012.03.008

    authors: Zhang J,Jeradi S,Strähle U,Akimenko MA

    更新日期:2012-05-15 00:00:00

  • Conditional knockout of fibronectin abrogates mouse mammary gland lobuloalveolar differentiation.

    abstract::Fibronectin (Fn) plays an important part in the branching morphogenesis of salivary gland, lung, and kidney. Here, we examine the effect of the conditional knockout of Fn in the mammary epithelium [Fn(MEp-/-)] on postnatal mammary gland development, using Cre-loxP-mediated gene knockout technology. Our data show that ...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2010.07.001

    authors: Liu K,Cheng L,Flesken-Nikitin A,Huang L,Nikitin AY,Pauli BU

    更新日期:2010-10-01 00:00:00

  • A protein of the sea urchin cortical granules is targeted to the fertilization envelope and contains an LDL-receptor-like motif.

    abstract::Cortical granules of eggs contain a population of heterogeneous proteins that are sequestered selectively within the cortical granule during oogenesis and that participate in the block to polyspermy during the fertilization reaction. To begin to understand the targeting mechanism of proteins to this organelle, we have...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.1995.1033

    authors: Wessel GM

    更新日期:1995-01-01 00:00:00

  • Deciphering the onychophoran 'segmentation gene cascade': Gene expression reveals limited involvement of pair rule gene orthologs in segmentation, but a highly conserved segment polarity gene network.

    abstract::The hallmark of the arthropods is their segmented body, although origin of segmentation, however, is unresolved. In order to shed light on the origin of segmentation we investigated orthologs of pair rule genes (PRGs) and segment polarity genes (SPGs) in a member of the closest related sister-group to the arthropods, ...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2013.07.010

    authors: Janssen R,Budd GE

    更新日期:2013-10-01 00:00:00

  • Xebf3 is a regulator of neuronal differentiation during primary neurogenesis in Xenopus.

    abstract::During primary neurogenesis in Xenopus, a cascade of helix--loop--helix (HLH) transcription factors regulates neuronal determination and differentiation. While XNeuroD functions at a late step in this cascade to regulate neuronal differentiation, the factors that carry out terminal differentiation are still unknown. W...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.2001.0230

    authors: Pozzoli O,Bosetti A,Croci L,Consalez GG,Vetter ML

    更新日期:2001-05-15 00:00:00

  • Molecular genetics of pecanex, a maternal-effect neurogenic locus of Drosophila melanogaster that potentially encodes a large transmembrane protein.

    abstract::In the absence of maternal expression of the pecanex gene, the embryo develops severe hyperneuralization similar to that characteristic of Notch mutant embryos. We have extended a previous molecular analysis of the chromosomal interval that encompasses pecanex by using additional deficiencies to localize the locus on ...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/0012-1606(89)90127-9

    authors: LaBonne SG,Sunitha I,Mahowald AP

    更新日期:1989-11-01 00:00:00

  • An antiserum (ES1) against a particulate form of extracellular matrix blocks the transition of cardiac endothelium into mesenchyme in culture.

    abstract::The epithelial-mesenchymal transition of cardiac endothelium is a critical developmental event in the formation of valvular and septal anlagen. We have demonstrated previously that this event can be mimicked in culture by treating atrioventricular canal (AV) endothelium with EDTA-soluble proteins extracted from embryo...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/0012-1606(91)90121-i

    authors: Mjaatvedt CH,Krug EL,Markwald RR

    更新日期:1991-06-01 00:00:00

  • Developmental patterning in the Caenorhabditis elegans hindgut.

    abstract::Developmental pattern formation allows cells within a tissue or organ to coordinate their development and establish cell types in relationship to one another. To better characterize the developmental patterning events within one organ, the C. elegans hindgut, we have analyzed the expression pattern of several genes us...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/s0012-1606(03)00352-x

    authors: Sewell ST,Zhang G,Uttam A,Chamberlin HM

    更新日期:2003-10-01 00:00:00

  • string(cdc25) and cyclin E are required for patterned histone expression at different stages of Drosophila embryonic development.

    abstract::Metazoan replication-dependent histone mRNAs accumulate to high levels during S phase as a result of an increase in the rate of histone gene transcription, pre-mRNA processing, and mRNA stability at the G1-S transition. However, relatively little is known about the contribution of these processes to histone expression...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2004.06.019

    authors: Lanzotti DJ,Kupsco JM,Marzluff WF,Duronio RJ

    更新日期:2004-10-01 00:00:00

  • Making sense of Dlx1 antisense RNA.

    abstract::Long non-coding RNAs (lncRNAs) have been recently recognized as a major class of regulators in mammalian systems. LncRNAs function by diverse and heterogeneous mechanisms in gene regulation, and are key contributors to development, neurological disorders, and cancer. This emerging importance of lncRNAs, along with rec...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2013.01.035

    authors: Kraus P,Sivakamasundari V,Lim SL,Xing X,Lipovich L,Lufkin T

    更新日期:2013-04-15 00:00:00

  • A role for Noggin in the development of oligodendrocyte precursor cells.

    abstract::Oligodendrocyte precursor cells (OPCs) can be differentiated in culture into either oligodendrocytes or type-2 astrocytes (2As), depending on the culture conditions. Whereas oligodendrocyte development can occur in the absence of inducing signals, 2A development apparently cannot. Fetal calf serum (FCS) and bone morph...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2003.11.013

    authors: Kondo T,Raff MC

    更新日期:2004-03-01 00:00:00

  • Intracellular pH increase driven by an Na+/H+ exchanger upon activation of surf clam oocytes.

    abstract::Intracellular pH (pHi) measurements were performed in surf clam (Spisula solidissima) oocytes before and after artificial activation or fertilization [evidenced by germinal vesicle breakdown (GVBD)] by the dimethyloxazolidinedione (DMO) and 2',7'-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein (BCECF) methods. Resul...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.1997.8682

    authors: Dubé F,Eckberg WR

    更新日期:1997-10-01 00:00:00

  • Testosterone-induced masculinization of the rat levator ani muscle during puberty.

    abstract::Previous study of the development of the levator ani muscle (LA) revealed that the sex difference in muscle fiber number is under the control of testosterone during the perinatal period. In this study, the development of the LA muscle was examined in both sexes to test the hypothesis that testosterone action determine...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.1994.1070

    authors: Joubert Y,Tobin C,Lebart MC

    更新日期:1994-03-01 00:00:00

  • Adhesive but not signaling activity of Drosophila N-cadherin is essential for target selection of photoreceptor afferents.

    abstract::Drosophila N-cadherin (CadN) is an evolutionarily conserved, atypical classical cadherin, which has a large complex extracellular domain and a catenin-binding cytoplasmic domain. We have previously shown that CadN regulates target selection of R7 photoreceptor axons. To determine the functional domains of CadN, we con...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2007.01.030

    authors: Yonekura S,Xu L,Ting CY,Lee CH

    更新日期:2007-04-15 00:00:00

  • Elf5 is a principal cell lineage specific transcription factor in the kidney that contributes to Aqp2 and Avpr2 gene expression.

    abstract::The mammalian kidney collecting ducts are critical for water, electrolyte and acid-base homeostasis and develop as a branched network of tubular structures composed of principal cells intermingled with intercalated cells. The intermingled nature of the different collecting duct cell types has made it challenging to id...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2017.02.007

    authors: Grassmeyer J,Mukherjee M,deRiso J,Hettinger C,Bailey M,Sinha S,Visvader JE,Zhao H,Fogarty E,Surendran K

    更新日期:2017-04-01 00:00:00

  • Sonic hedgehog differentially regulates expression of GLI and GLI3 during limb development.

    abstract::Sonic hedgehog is a secreted factor regulating patterning of the anterior-posterior axis in the developing limb. The signaling pathway mediating the transduction of the signal is still poorly understood. In Drosophila several genes are known to act downstream of hedgehog, the fly homolog of Sonic hedgehog. An importan...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.1996.0300

    authors: Marigo V,Johnson RL,Vortkamp A,Tabin CJ

    更新日期:1996-11-25 00:00:00

  • Differential expression of Eph receptors and ephrins correlates with the formation of topographic projections in primary and secondary visual circuits of the embryonic chick forebrain.

    abstract::Repulsion plays a fundamental role in the establishment of a topographic map of the chick retinotectal projections. This has been highlighted by studies demonstrating the role of opposing gradients of the EphA3 receptor tyrosine kinase on retinal axons and two of its ligands, ephrin-A2 and ephrin-A5, in the tectum. We...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.2001.0268

    authors: Marín O,Blanco MJ,Nieto MA

    更新日期:2001-06-15 00:00:00

  • Organoid technology for retinal repair.

    abstract::A major cause for vision impairment and blindness in industrialized countries is the loss of the light-sensing retinal tissue in the eye. Photoreceptor damage is one of the main characteristics found in retinal degeneration diseases, such as Retinitis Pigmentosa or age-related macular degeneration. The lack of effecti...

    journal_title:Developmental biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.ydbio.2017.09.028

    authors: Llonch S,Carido M,Ader M

    更新日期:2018-01-15 00:00:00

  • Integration of comprehensive 3D microCT and signaling analysis reveals differential regulatory mechanisms of craniofacial bone development.

    abstract::Growth factor signaling regulates tissue-tissue interactions to control organogenesis and tissue homeostasis. Specifically, transforming growth factor beta (TGFβ) signaling plays a crucial role in the development of cranial neural crest (CNC) cell-derived bone, and loss of Tgfbr2 in CNC cells results in craniofacial s...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2015.02.010

    authors: Ho TV,Iwata J,Ho HA,Grimes WC,Park S,Sanchez-Lara PA,Chai Y

    更新日期:2015-04-15 00:00:00

  • cMeso-1, a novel bHLH transcription factor, is involved in somite formation in chicken embryos.

    abstract::The segmentation of somites from the paraxial mesoderm is a crucial event in vertebrate embryonic development; however, the mechanisms underlying this process are not well understood. In a yeast two-hybrid screen we have identified the novel basic-helix-loop-helix (bHLH) protein cMeso-1 which is expressed in the preso...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.1998.8919

    authors: Buchberger A,Seidl K,Klein C,Eberhardt H,Arnold HH

    更新日期:1998-07-15 00:00:00

  • Synthesis and distribution of carbohydrate chains in cleavage-stage mouse embryos carrying the t12 lethal mutation.

    abstract::Carbohydrate chains on the t12 mutant embryos were analyzed. No abnormalities of the synthesis of the carbohydrate chains were observed in the t12 homozygotes until the late morula stage, when radiolabeled carbohydrate chains were analyzed by Sephadex G-50 column chromatography. Furthermore, polarization of the Con A ...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/0012-1606(88)90309-0

    authors: Iwakura Y,Nozaki M

    更新日期:1988-08-01 00:00:00

  • DM-GRASP/ALCAM/CD166 is required for cardiac morphogenesis and maintenance of cardiac identity in first heart field derived cells.

    abstract::Vertebrate heart development requires specification of cardiac precursor cells, migration of cardiac progenitors as well as coordinated cell movements during looping and septation. DM-GRASP/ALCAM/CD166 is a member of the neuronal immunoglobulin domain superfamily of cell adhesion molecules and was recently suggested t...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2008.06.013

    authors: Gessert S,Maurus D,Brade T,Walther P,Pandur P,Kühl M

    更新日期:2008-09-01 00:00:00

  • Evidence that protein kinase C (PKC) participates in the meiosis I to meiosis II transition in mouse oocytes.

    abstract::Oocytes from LTXBO mice exhibit a delayed entry into anaphase I and frequently enter interphase after the first meiotic division. This unique oocyte model was used to test the hypothesis that protein kinase C (PKC) may regulate the meiosis I-to-meiosis II transition. PKC activity was detected in LTXBO oocytes at proph...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1006/dbio.2001.0311

    authors: Viveiros MM,Hirao Y,Eppig JJ

    更新日期:2001-07-15 00:00:00

  • The exon junction complex is required for stem and progenitor cell maintenance in planarians.

    abstract::Named for its assembly near exon-exon junctions during pre-mRNA splicing, the exon junction complex (EJC) regulates multiple aspects of RNA biochemistry, including export of spliced mRNAs from the nucleus and translation. Transcriptome analyses have revealed broad EJC occupancy of spliced metazoan transcripts, yet inh...

    journal_title:Developmental biology

    pub_type: 杂志文章

    doi:10.1016/j.ydbio.2019.09.010

    authors: Kimball C,Powers K,Dustin J,Poirier V,Pellettieri J

    更新日期:2020-01-01 00:00:00