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Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jsre.2001.6318openalex-snapshot

TIMP-1 Overexpression in Pancreatic Cancer Attenuates Tumor Growth, Decreases Implantation and Metastasis, and Inhibits Angiogenesis

inferredcites →https://doi.org/10.1007/3-540-27683-1_10openalex-snapshot

Mutable Collagenous Tissue: Overview and Biotechnological Perspective

inferredcites →https://doi.org/10.1016/j.ajpath.2011.07.035openalex-snapshot

Endogenous Angiogenesis Inhibitor Blocks Tumor Growth via Direct and Indirect Effects on Tumor Microenvironment

inferredcites →https://doi.org/10.1016/j.cell.2010.03.015openalex-snapshot

Matrix Metalloproteinases: Regulators of the Tumor Microenvironment

inferredcites →https://doi.org/10.1016/j.critrevonc.2003.09.008openalex-snapshot

TIMPs as multifacial proteins

inferredcites →https://doi.org/10.1016/j.ejogrb.2009.02.036openalex-snapshot

Cervical ripening and insufficiency: From biochemical and molecular studies to in vivo clinical examination

inferredcites →https://doi.org/10.1016/s0167-4838(99)00279-4openalex-snapshot

Tissue inhibitors of metalloproteinases: evolution, structure and function

inferredcites →https://doi.org/10.1016/s0945-053x(02)00090-2openalex-snapshot

Purification, characterization and cloning of tensilin, the collagen-fibril binding and tissue-stiffening factor from Cucumaria frondosa dermis

inferredcites →https://doi.org/10.1023/a:1026348808069openalex-snapshot

Computational Sequence Analysis of the Tissue Inhibitor of Metalloproteinase Family

inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

inferredcites →https://doi.org/10.1080/10236248409387032openalex-snapshot

Variable tensility in echinoderm collagenous tissues: A review

inferredcites →https://doi.org/10.1080/10635150701613783openalex-snapshot

Estimating Divergence Times in Large Phylogenetic Trees

inferredcites →https://doi.org/10.1080/10635150802429642openalex-snapshot

A Rapid Bootstrap Algorithm for the RAxML Web Servers

inferredcites →https://doi.org/10.1086/bblv221n3p280openalex-snapshot

Mechanical Mutability in Connective Tissue of Starfish Body Wall

inferredcites →https://doi.org/10.1093/bioinformatics/17.9.847openalex-snapshot

InterProScan – an integration platform for the signature-recognition methods in InterPro

inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btv428openalex-snapshot

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

inferredcites →https://doi.org/10.1093/nar/30.1.276openalex-snapshot

The Pfam Protein Families Database

inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

inferredcites →https://doi.org/10.1093/nar/gki442openalex-snapshot

InterProScan: protein domains identifier

inferredcites →https://doi.org/10.1093/nar/gkm977openalex-snapshot

The 20 years of PROSITE

inferredcites →https://doi.org/10.1093/nar/gkp1019openalex-snapshot

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

inferredcites →https://doi.org/10.1093/nar/gkp985openalex-snapshot

The Pfam protein families database

inferredcites →https://doi.org/10.1093/nar/gku1243openalex-snapshot

The InterPro protein families database: the classification resource after 15 years

inferredcites →https://doi.org/10.1093/sysbio/sys078openalex-snapshot

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

inferredcites →https://doi.org/10.1098/rspb.2000.1278openalex-snapshot

Testing macro–evolutionary models using incomplete molecular phylogenies

inferredcites →https://doi.org/10.1098/rspb.2014.0479openalex-snapshot

Phylogenomic analysis of echinoderm class relationships supports Asterozoa

inferredcites →https://doi.org/10.1101/gr.772403openalex-snapshot

PANTHER: A Library of Protein Families and Subfamilies Indexed by Function

inferredcites →https://doi.org/10.1111/j.1096-3642.2001.tb00622.xopenalex-snapshot

Phylogeny of the Apodan Holothurians (Echinodermata) inferred from morphology

inferredcites →https://doi.org/10.1111/j.1469-185x.1984.tb00409.xopenalex-snapshot

CONNECTIVE TISSUE CATCH IN ECHINODERMS

inferredcites →https://doi.org/10.1139/z66-109openalex-snapshot

ANAL PORES IN LEPTOSYNAPTA CLARKI (APODA)

inferredcites →https://doi.org/10.1145/2335755.2335842openalex-snapshot

Trinity RNA-Seq assembler performance optimization

inferredcites →https://doi.org/10.1242/jeb.02178openalex-snapshot

Tensilin-like stiffening protein fromHolothuria leucospilotadoes not induce the stiffest state of catch connective tissue

inferredcites →https://doi.org/10.1371/journal.pone.0049016openalex-snapshot

Matrix Metalloproteinases in a Sea Urchin Ligament with Adaptable Mechanical Properties

inferredcites →https://doi.org/10.1371/journal.pone.0085644openalex-snapshot

Softenin, a Novel Protein That Softens the Connective Tissue of Sea Cucumbers through Inhibiting Interaction between Collagen Fibrils

inferredcites →https://doi.org/10.1371/journal.pone.0120339openalex-snapshot

Mechanical Properties of the Compass Depressors of the Sea-Urchin Paracentrotus lividus (Echinodermata, Echinoidea) and the Effects of Enzymes, Neurotransmitters and Synthetic Tensilin-Like Protein

inferredcites →https://doi.org/10.3109/03008207.2013.867339openalex-snapshot

Normalization of the tumor microenvironment: evidence for tissue inhibitor of metalloproteinase-2 as a cancer therapeutic

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3390/md13031202openalex-snapshot

Anticancer Activity of Sea Cucumber Triterpene Glycosides

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.11646/zootaxa.4995.1.2zenodo-depositor-declared

Catalogue of living crinoids (Echinodermata: Crinoidea) from Brazil

inferred← citeshttps://doi.org/10.1007/s00441-020-03201-0openalex-snapshot

Extracellular matrix gene expression during arm regeneration in Amphiura filiformis

inferred← citeshttps://doi.org/10.1007/s12526-021-01194-9openalex-snapshot

Brooding comatulids from the southwestern Atlantic, Argentina (Echinodermata: Crinoidea)

inferred← citeshttps://doi.org/10.1016/b978-0-323-95377-1.00041-2openalex-snapshot

Mutable collagenous tissues in sea cucumbers

inferred← citeshttps://doi.org/10.1016/j.dci.2021.104298openalex-snapshot

Tissue inhibitor of metalloproteinases 1 is involved in ROS-mediated inflammation via regulating matrix metalloproteinase 1 expression in the sea cucumber Apostichopus japonicus

inferred← citeshttps://doi.org/10.1016/j.fsi.2023.108593openalex-snapshot

AjTGFβ alleviates V. splendidus-induced inflammation through SMADs pathway in Apostichopus japonicus

inferred← citeshttps://doi.org/10.1016/j.isci.2023.108579openalex-snapshot

Tracing the evolution of tissue inhibitor of metalloproteinases in Metazoa with the Pteria penguin genome

inferred← citeshttps://doi.org/10.1016/j.matbio.2022.02.006openalex-snapshot

Molecular mechanisms mediating stiffening in the mechanically adaptable connective tissues of sea cucumbers

inferred← citeshttps://doi.org/10.1038/s41467-017-00679-1openalex-snapshot

Photo-triggered solvent-free metamorphosis of polymeric materials

inferred← citeshttps://doi.org/10.1039/9781839161124-00001openalex-snapshot

The Mutable Collagenous Tissue of Echinoderms: From Biology to Biomedical Applications

inferred← citeshttps://doi.org/10.1098/rsos.251924openalex-snapshot

Phylogenomics of extant Crinoidea (Echinodermata) reveals extensive morphological homoplasies and a Permian origin

inferred← citeshttps://doi.org/10.1098/rspb.2023.0988openalex-snapshot

Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea

inferred← citeshttps://doi.org/10.1186/s12859-016-0883-2openalex-snapshot

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms

inferred← citeshttps://doi.org/10.1186/s12863-022-01090-6openalex-snapshot

EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

inferred← citeshttps://doi.org/10.1242/dev.205344openalex-snapshot

BMP signaling regulates dorsal skeletal growth in the sea urchin embryo

inferred← citeshttps://doi.org/10.1371/journal.pone.0195836openalex-snapshot

Molecular mechanisms of fission in echinoderms: Transcriptome analysis

inferred← citeshttps://doi.org/10.3390/cells10092331openalex-snapshot

Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Echinoderms: Structure and Possible Functions

inferred← citeshttps://doi.org/10.3390/encyclopedia5040185openalex-snapshot

Strength in Weakness: The Mutable Collagenous Tissue of Echinoderms

inferred← citeshttps://doi.org/10.3390/genes12020250openalex-snapshot

Molecular Aspects of Regeneration Mechanisms in Holothurians

inferred← citeshttps://doi.org/10.3390/genes12081292openalex-snapshot

Expression of Piwi, MMP, TIMP, and Sox during Gut Regeneration in Holothurian Eupentacta fraudatrix (Holothuroidea, Dendrochirotida)

inferred← citeshttps://doi.org/10.3390/md21030140openalex-snapshot

Possible Mechanisms of Stiffness Changes Induced by Stiffeners and Softeners in Catch Connective Tissue of Echinoderms

inferred← citeshttps://doi.org/10.3390/md21070417openalex-snapshot

Extracellular Matrix of Echinoderms

inferred← citeshttps://doi.org/10.6084/m9.figshare.21385873openalex-snapshot

Additional file 2 of EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

inferred← citeshttps://doi.org/10.6084/m9.figshare.21385876openalex-snapshot

Additional file 3 of EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

inferred← citeshttps://doi.org/10.6084/m9.figshare.21385879openalex-snapshot

Additional file 4 of EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms

inferred← citeshttps://doi.org/10.7554/elife.72460openalex-snapshot

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

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