CellMontage: Similar Expression Profile Search Server

Fujibuchi, Wataru; Kiseleva, Larisa; Taniguchi, Tadatsugu; Harada, Hajime; Horton, Paul

doi:10.1093/bioinformatics/btn101

Cited by 12 publications

(13 citation statements)

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“…The Profile search (9, 10) facility of the spotfire software was used to isolate clusters of genes exhibiting a time‐course profile similar to that of Prnp . This is a statistical tool used to isolate a cluster of genes with closely similar time‐course expression profiles.…”

Section: Methodsmentioning

confidence: 99%

Expression of prion gene and presence of prion protein during development of mouse molar tooth germ

Khan

Press

Sehic

et al. 2010

European J Oral Sciences

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In order to gain insight into possible cellular functions of the prion protein (PrP) during normal development, the expression of Prnp (encoding the PrP) and the distribution of the PrP were studied in murine tooth germs. Expression of Prnp in the mouse first molar tooth germ was highly dynamic, increasing several-fold during the secretory phase of odontogenesis, exhibiting a time-course of expression similar to that of genes coding for other extracellular proteins [e.g. enamel matrix proteins (Amelx, Ambn, Enam), Aplp1, Clstn1, and Clu]. Western blot analysis suggested that the amounts of PrP and amyloid beta (A4) precursor-like protein 1 (APLP1) in the tooth germ followed time-courses similar to those of the corresponding mRNAs. Immunohistochemical studies of the distribution of PrP in murine molar and incisor tooth germs at embryonic day (E)18.5 suggested that this protein was located in the cervical loop, outer enamel epithelium, pre-ameloblasts, and dental papilla. Different degrees of immunolabelling of pre-ameloblasts on the mesial and distal aspects of a lower molar cusp may be related to different enamel configurations on the two aspects. It is concluded that the dynamic patterns of expression of Prnp, and of distribution of PrP, suggest that PrP may have functions during secretory odontogenesis, perhaps in relation to amelogenesis.

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Section: Methodsmentioning

confidence: 99%

Expression of prion gene and presence of prion protein during development of mouse molar tooth germ

Khan

Press

Sehic

et al. 2010

European J Oral Sciences

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“…To investigate the functional diversity among the human genes in the AIS subfamilies, we used large-scale microarray expression profiles of various human organs and tissues [ 16 ]. For a broad overview of tissue- and organ-specific expression, we used a classification scheme (see Additional File 8 ) that is a simplified version of Cell Catalogue [ 17 ] to classify all 79 tissues and organs used in the microarray data into 11 system-level function categories; we then assigned these categories to the human genes in the AIS subfamilies: if a gene was specifically expressed in at least one of the tissues or organs in a system-level function category, then the system-level function category was assigned to the gene (see Additional File 9 ). We then assigned a system-level function category to an AIS subfamily if the AIS subfamily included at least one member gene having the system-level function category.…”

Section: Resultsmentioning

confidence: 99%

Expansion of signaling genes for adaptive immune system evolution in early vertebrates

Okada

Asai

2008

BMC Genomics

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“…Similar idea is used in a few studies to produce new biological hypotheses by associating the current experiment with similar previous experiments, thus confirming the usability of the approach in practice [4][5][6][7][8][9]. Spearman correlation coefficient is considered as a faster alternative for comparing two profiles [10][11]. A variety of web servers are available with similar objective.…”

Section: Introductionmentioning

confidence: 84%

Content-Based Search on Time-Series Microarray Databases

Hayran

Ogul

Özkoç

2014

2014 25th International Workshop on Database and Expert Systems Applications

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We study, for the first time, the problem of content-based searching of time-series microarray experiments in large-scale gene expression databases. The problem is approached as an information retrieval task where an entire experiment is taken as the query and searched through a collection of previous experiments. The relevant experiments are required to be retrieved based on the content similarity rather than their meta-data descriptions. A comparison of different fingerprinting and distance computation schemes is presented over a retrieval framework based on the differential expression of genes in varying time points.

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CellMontage: Similar Expression Profile Search Server

Cited by 12 publications

References 0 publications

Expression of prion gene and presence of prion protein during development of mouse molar tooth germ

Expression of prion gene and presence of prion protein during development of mouse molar tooth germ

Expansion of signaling genes for adaptive immune system evolution in early vertebrates

Content-Based Search on Time-Series Microarray Databases

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