Evidence map›Paper›PMID 25382412›Full record

ArticleScientific reports2014

Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain.

Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Akira Sato, Teiichi Furuichi, Hideo Yokota

Abstract read
In one paragraph

Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Yuko Okamura-Oho1] Brain Research Network (BReNt), 2-2-41 Sakurayama, Zushi-shi, Kanagawa, 249-0005, Japan [2] Image Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Kazuro ShimokawaDepartment of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-chou Aoba-ku Sendai-shi Miyagi, 980-8573, Japan.
Masaomi NishimuraImage Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Satoko TakemotoImage Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.
Akira SatoDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan.
Teiichi FuruichiDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan.
Hideo YokotaImage Processing Research Team, Extreme Photonics Research Group, RIKEN Center for Advanced Photonics, 2-1 Hirosawa Wako-shi Saitama, 351-0198, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Using a recently invented technique for gene expression mapping in the whole-anatomy context, termed transcriptome tomography, we have generated a dataset of 36,000 maps of overall gene expression in the adult-mouse brain. Here, using an informatics approach, we identified a broad co-expression network that follows an inverse power law and is rich in functional interaction and gene-ontology terms. Our framework for the integrated analysis of expression maps and graphs of co-expression networks revealed that groups of combinatorially expressed genes, which regulate cell differentiation during development, were present in the adult brain and each of these groups was associated with a discrete cell types. These groups included non-coding genes of unknown function. We found that these genes specifically linked developmentally conserved groups in the network. A previously unrecognized robust expression pattern covering the whole brain was related to the molecular anatomy of key biological processes occurring in particular areas.

Indexed as

Gene Expression ProfilingGene Regulatory NetworksTranscriptomeAnimalsBrainComputational BiologyHomeodomain ProteinsMaleMiceOrgan SpecificityTranscription FactorsHomeodomain ProteinsTranscription Factors

Identifiers

PMID25382412
PMCPMC4225549

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.