CoChat
Sign Up
Cited by 202

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data

Freeman, Tom C, Goldovsky, Leon, Brosch, Markus, van Dongen, Stijn, Mazière, Pierre, Grocock, Russell J, Freilich, Shiri, Thornton, Janet +1 more·2007·PLoS Computational Biology
DOI 10.1371/journal.pcbi.0030206PMC PMC2041979
Open this paper in CoChat — free account

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pcbi.0030206

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • In the miRNA expression network, 502 nodes representing miRNAs were connected by 3,369 weighted, undirected edges representing correlations of at least 0.6 between expression patterns.

    “in which 502 nodes representing miRNAs were connected by 3,369 weighted, undirected edges representing correlations of at least 0.6 between expression patterns.”

    From An integrated expression atlas of miRNAs and their promoters in human and mouse (2017) · cites this paper as [28]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 35

  1. Janssen P Audit B Cases I Darzentas N Goldovsky L 2003 Beyond 100 genomes Genome Biol 4 402 12734008 PMC156585
  2. Reed JL Famili I Thiele I Palsson BO 2006 Towards multidimensional genome annotation Nat Rev Genet 7 130 141 16418748
  3. Kitano H 2002 Computational systems biology Nature 420 206 210 12432404
  4. Nurse P 2003 Systems biology: Understanding cells Nature 424 883 12931164
  5. Cassman M 2005 Barriers to progress in systems biology Nature 438 1079 16371982
  6. Enright AJ Kunin V Ouzounis CA 2003 Protein families and TRIBES in genome sequence space Nucleic Acids Res 31 4632 4638 12888524 PMC169885
  7. Enright AJ Van Dongen S Ouzounis CA 2002 An efficient algorithm for large-scale detection of protein families Nucleic Acids Res 30 1575 1584 11917018 PMC101833
  8. Li L Stoeckert CJ Jr Roos DS 2003 OrthoMCL: Identification of ortholog groups for eukaryotic genomes Genome Res 13 2178 2189 12952885 PMC403725
  9. Bader GD Enright AJ 2005 Biomolecular interactions and biological pathways Baxevanis AD Bioinformatics: A practical analysis of genes and proteins New York John Wiley 540
  10. Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D 2002 Network motifs: Simple building blocks of complex networks Science 298 824 827 12399590
  11. Jeong H Mason SP Barabasi AL Oltvai ZN 2001 Lethality and centrality in protein networks Nature 411 41 42 11333967
  12. Almudevar A Klebanov LB Qiu X Salzman P Yakovlev AY 2006 Utility of correlation measures in analysis of gene expression NeuroRx 3 384 395 16815221 PMC3593386
  13. Lee HK Hsu AK Sajdak J Qin J Pavlidis P 2004 Coexpression analysis of human genes across many microarray data sets Genome Res 14 1085 1094 15173114 PMC419787
  14. Franke L Bakel H Fokkens L de Jong ED Egmont-Petersen M 2006 Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes Am J Hum Genet 78 1011 1025 16685651 PMC1474084
  15. Kim SK Lund J Kiraly M Duke K Jiang M 2001 A gene expression map for Caenorhabditis elegans Science 293 2087 2092 11557892
  16. Tsaparas P Marino-Ramirez L Bodenreider O Koonin EV Jordan IK 2006 Global similarity and local divergence in human and mouse gene co-expression networks BMC Evol Biol 6 70 16968540 PMC1601971
  17. Wang Y Joshi T Zhang XS Xu D Chen L 2006 Inferring gene regulatory networks from multiple microarray datasets Bioinformatics 22 2413 2420 16864593
  18. Su AI Wiltshire T Batalov S Lapp H Ching KA 2004 A gene atlas of the mouse and human protein-encoding transcriptomes Proc Natl Acad Sci U S A 101 6062 6067 15075390 PMC395923
  19. van Noort V Snel B Huynen MA 2003 Predicting gene function by conserved co-expression Trends Genet 19 238 242 12711213
  20. Wu Z Irizarry RA 2005 Stochastic models inspired by hybridization theory for short oligonucleotide arrays J Comput Biol 12 882 893 16108723
  21. Wu Z Irizarry RA 2004 Preprocessing of oligonucleotide array data Nat Biotechnol 22 656 658 15175677
  22. Liu WM Mei R Di X Ryder TB Hubbell E 2002 Analysis of high density expression microarrays with signed-rank call algorithms Bioinformatics 18 1593 1599 12490443
  23. Hubbell E Liu WM Mei R 2002 Robust estimators for expression analysis Bioinformatics 18 1585 1592 12490442
  24. van Dongen S 2000 Graph clustering by flow simulation [PhD dissertation] Utrecht (The Netherlands) University of Utrecht 169 p. Available at: http://igitur-archive.library.uu.nl/dissertations/1895620/inhoud.htm. Accessed 27 September 2007.
  25. Pereira-Leal JB Enright AJ Ouzounis CA 2004 Detection of functional modules from protein interaction networks Proteins 54 49 57 14705023
  26. Harris MA Clark J Ireland A Lomax J Ashburner M 2004 The Gene Ontology (GO) database and informatics resource Nucleic Acids Res 32 D258 D261 14681407 PMC308770
  27. Freilich S Massingham T Bhattacharyya S Ponsting H Lyons PA 2005 Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins Genome Biol 6 R56 15998445 PMC1175987
  28. Freilich S Massingham T Blanc E Goldovsky L Thornton JM 2006 Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins Genome Biol 7 R89 17029626 PMC1794571
  29. Ning Z Cox AJ Mullikin JC 2001 SSAHA: A fast search method for large DNA databases Genome Res 11 1725 1729 11591649 PMC311141
  30. Watts DJ Strogatz SH 1998 Collective dynamics of “small-world” networks Nature 393 440 442 9623998
  31. Yeger-Lotem E Sattath S Kashtan N Itzkovitz S Milo R 2004 Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction Proc Natl Acad Sci U S A 101 5934 5939 15079056 PMC395901
  32. Hermjakob H Montecchi-Palazzi L Lewington C Mudali S Kerrien S 2004 IntAct: An open source molecular interaction database Nucleic Acids Res 32 D452 D455 14681455 PMC308786
  33. Lehner B Fraser AG 2004 A first-draft human protein-interaction map Genome Biol 5 R63 15345047 PMC522870
  34. von Mering C Huynen M Jaeggi D Schmidt S Bork P 2003 STRING: A database of predicted functional associations between proteins Nucleic Acids Res 31 258 261 12519996 PMC165481
  35. Zeeberg BR Feng W Wang G Wang MD Fojo AT 2003 GoMiner: A resource for biological interpretation of genomic and proteomic data Genome Biol 4 R28 12702209 PMC154579

Cited by

Sorted by citations

Authors
Freeman, T. C., Goldovsky, L., Brosch, M., van Dongen, S., Mazière, P., Grocock, R. J., Freilich, S., Thornton, J., & Enright, A. J.
Venue
PLoS Computational Biology
Publisher
Public Library of Science (PLoS)
Published
2007-10-26
Volume
3
Issue
10
Pages
e206
ISSN
1553-7358
DOI
10.1371/journal.pcbi.0030206
PMC
PMC2041979
Cited by
202
References
1
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review