Evidence map›Paper›PMID 26003204›Full record

ArticleBMC bioinformatics2015

NetworkPainter: dynamic intracellular pathway animation in Cytobank.

Jonathan R Karr, Harendra Guturu, Edward Y Chen, Stuart L Blair, Jonathan M Irish, Nikesh Kotecha, Markus W Covert

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Cell size assays for mass cytometry.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2017
    Article
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.

Jonathan R KarrGraduate Program in Biophysics, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA. jkarr@stanfordalumni.org.
Harendra GuturuDepartment of Electrical Engineering, Stanford University, 279 Campus Drive West, MC 5329, Stanford, CA, 94305, USA. hguturu@stanford.edu.
Edward Y ChenDepartment of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA. edchen@alumni.stanford.edu.
Stuart L BlairCytobank Inc, 821 West El Camino Real, Mountain View, CA, 94040, USA. stu@cytobank.org.
Jonathan M IrishDepartment of Medicine, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA. jonathan.irish@vanderbilt.edu.
Nikesh KotechaGraduate Program in Biomedical Informatics, Stanford University, 269 Campus Drive West, MC 5175, Stanford, CA, 94305, USA. nikesh@cytobank.org.
Markus W CovertDepartment of Bioengineering, Stanford University, 443 Via Ortega, MC 4245, Stanford, CA, 94305, USA. mcovert@stanford.edu.

Funding

TRAINING & OUTREACH COREP50GM107615 · NIGMS · STANFORD UNIVERSITY · PI FERRELL, JAMES E. · 2013 to 2017
$10.9M
Web Software for Drug Targeting Signaling Networks in Primary Cell SubsetsR44GM096579 · NIGMS · CYTOBANK, INC. · PI CRAFORD, DAVID · 2014 to 2015
$1.5M
PEARLS DisseminationR18DP001150 · DP · UNIVERSITY OF WASHINGTON · PI SNOWDEN, MARK · 2007 to 2009
$1.2M
Combining Computational and Experimentation to Interrogate NF-kappaB SignalingR00CA125994 · NCI · STANFORD UNIVERSITY · PI COVERT, MARKUS W · 2009 to 2011
$740k
Targeting the B Cell Receptor Signaling Network in LymphomaR00CA143231 · NCI · VANDERBILT UNIVERSITY · PI IRISH, JONATHAN MICHAEL · 2012 to 2014
$715k
Combining Computational and Experimentation to Interrogate NF-kappaB SignalingK99CA125994 · NCI · STANFORD UNIVERSITY · PI COVERT, MARKUS W · 2007 to 2008
$275k
Secure Web-Based Flow Cytometry in Clinical Use and Translational ResearchR43AI094929 · NIAID · CYTOBANK, INC. · PI KOTECHA, NIKESH · 2012 to 2012
$268k
Web Software for Drug Targeting Signaling Networks in Primary Cell SubsetsR43GM096579 · NIGMS · CYTOBANK, INC. · PI KOTECHA, NIKESH · 2011 to 2011
$150k
Targeting the B Cell Receptor Signaling Network in LymphomaK99CA143231 · NCI · STANFORD UNIVERSITY · PI IRISH, JONATHAN MICHAEL · 2009 to 2009
$136k
NCCDPHP CDC HHS 5DP1LM01150-05NCI NIH HHS CA125994-01A1NCI NIH HHS CA143231NCI NIH HHS K99 CA125994NCI NIH HHS K99 CA143231NCI NIH HHS R00 CA125994NCI NIH HHS R00 CA143231NHLBI NIH HHS HHSN268201300037CNIAID NIH HHS R43 AI094929NIGMS NIH HHS 1P50GM107615NIGMS NIH HHS P50 GM107615NIGMS NIH HHS R43 GM096579NIGMS NIH HHS R44 GM096579
6 · The paper itself

Abstract

backgroundHigh-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data.

resultsWe developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point.

conclusionNetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.

Indexed as

InternetSignal TransductionSoftwareComputational BiologyComputer SimulationCytoplasmDatabase Management SystemsDatabases, FactualFlow CytometryHumansLeukocytes, Mononuclear

Identifiers

PMID26003204
PMCPMC4491883

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.