The DOI matches its Crossref record; 60 of the 61 references it cites were found in a registry or an index; none of the 49 sources its claims cite is checked for support yet.
Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism
Open accessAbstract
Autism spectrum disorder (ASD) involves substantial genetic contributions. These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood. Here, through post-mortem genome-wide transcriptome analysis of the largest cohort of samples analysed so far, to our knowledge, we interrogate the noncoding transcriptome, alternative splicing, and upstream molecular regulators to broaden our understanding of molecular convergence in ASD. Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes. Our data suggest that SOX5, a transcription factor involved in neuron fate specification, contributes to this reduction in regional differences. We further demonstrate that a genetically defined subtype of ASD, chromosome 15q11.2-13.1 duplication syndrome (dup15q), shares the core transcriptomic signature observed in idiopathic ASD. Co-expression network analysis reveals that individuals with ASD show age-related changes in the trajectory of microglial and synaptic function over the first two decades, and suggests that genetic risk for ASD may influence changes in regional cortical gene expression. Our findings illustrate how diverse genetic perturbations can lead to phenotypic convergence at multiple biological levels in a complex neuropsychiatric disorder.
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“Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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In the paper
“Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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In the paper
“Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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“We performed a classification analysis to confirm that gene expression in ASD could separate samples by disease status (Extended Data Fig. 2a) and confirmed the technical quality of our data with qRT–PCR (Extended Data Fig. 2b, c).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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“Therefore, we next investigated whether the shared splicing signature in ASD could be explained by perturbations in splicing factors known to be important in nervous system function8,14 (Extended Data Fig. 4j), and found high correlations between splicing factor expression and differential splicing in the cortex (Fig. 1f) but not the cerebellum (Fig. 1g).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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“We next evaluated enrichment of the gene sets for pathways and cell types (Extended Data Fig. 2d, e), and found that the downregulated set was enriched in genes expressed in neurons and involved in neuronal pathways, including PVALB and SYT2, which are highly expressed in interneurons; by contrast, the upregulated gene set was enriched in genes expressed in microglia and astrocytes8.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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“As a group, these lncRNAs are enriched in the brain relative to other tissues (Extended Data Fig. 2l, m) and most that have been evaluated across species exhibit primate-specific expression patterns in the brain11, which we confirm for several transcripts (Supplementary Information, Extended Data Fig. 3a–h).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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“The lack of significant DGE in the cerebellum is explained by the fact that changes in expression were consistently stronger in the cortex than in the cerebellum (Extended Data Fig. 2h), which suggests that the cortex is more selectively vulnerable to these transcriptomic alterations.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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“We found a significant differential splicing signal over background in the cortex (1,127 differential splicing events in 833 genes; Methods), but not in the cerebellum (P distributions in Extended Data Fig. 4b, c).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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In the paper
“We found a significant differential splicing signal over background in the cortex (1,127 differential splicing events in 833 genes; Methods), but not in the cerebellum (P distributions in Extended Data Fig. 4b, c).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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- It may state two separate claims as one. 32
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In the paper
“Moreover, alterations in dup15q cortex were of greater magnitude and more homogeneous than those observed in idiopathic ASD cortex (Fig. 3d, Extended Data Fig. 7f, g).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaincorrelationaln = 9- Asserted: passes — The authors put it forward as true.
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In the paper
“We confirmed this in our larger cohort and identified 523 genes that differed significantly in expression between the frontal cortex and the temporal cortex in control subjects, but not those with ASD (Fig. 2a); we refer to these genes as the ‘attenuated cortical patterning’ (ACP) set (Extended Data Fig. 6a).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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In the paper
“Although there was no significant DGE in the cerebellum (FDR < 0.05, P distributions in Fig. 1b), similar to observations in a smaller cohort8, there was a replication signal in the cerebellum and overall concordance between ASD-related fold changes in the cortex and cerebellum (Extended Data Fig. 2f–h).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [8] Voineagu, I. et al. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474, 380–384 (2011) source
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In the paper
“Analysis of DGE in the cerebellum confirmed a weaker signal than in the cortex and demonstrated that cis changes in dup15q cerebellum (Extended Data Fig. 7h–j) were more concordant with the cortex than trans changes (Extended Data Fig. 7k, l), further supporting the observation that the cortex is selectively vulnerable to transcriptomic alteration in ASD.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
boostedcorrelationaln = 9- Asserted: passes — The authors put it forward as true.
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In the paper
“Of the six modules associated with ASD, three were upregulated and three were downregulated, and each showed significant cell-type enrichment (Fig. 4a, b).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Among the transcription factors identified, SOX5 was of particular interest because of its known role in mammalian corticogenesis23,24, its sole membership in the ACP set, and its correlation with predicted targets in the brains of control subjects, which is lost in ASD (Fig. 2b–d).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
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In the paper
“Several other ASD-associated modules showed a weaker common variant signal for ASD, including CTX.M16, which also shows a signal for schizophrenia polygenic risk.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Significant upregulation in the 15q11.1–13.2 region (cis) was evident in duplication carriers, but not in idiopathic ASD (Fig. 3a).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plainn = 9- Asserted: passes — The authors put it forward as true.
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In the paper
“Remarkably, CTX.M24 was significantly enriched for lncRNAs, genes expressed highly during fetal cortical development, and genes harbouring protein-disrupting mutations found in ASD, suggesting that lncRNAs will be important targets for investigation in ASD10,25 (FDR < 0.05, Extended Data Fig. 9a, g).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“We also found preservation of most cortex modules in the cerebellum, but with weaker associations to ASD (Extended Data Fig. 10a–h, Supplementary Table 4), consistent with the DGE analysis showing that ASD-related changes are substantially smaller in the cerebellum.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“We highlight two primate-specific lncRNAs, LINC00693 and LINC00689. Both interact with miRNA processing complexes and are typically downregulated during development12, but are upregulated in ASD cortex (Fig. 1c, d, Extended Data Fig. 2n).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [12] Jaffe, A. E. et al. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat. Neurosci. 18, 154–161 (2015) source
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In the paper
“We confirmed that a significant proportion of ACP genes are regulated by SOX5 by overexpressing it in human neural progenitors. SOX5 induced synaptic genes and repressed cell proliferation (Fig. 2e), and predicted SOX5 targets exhibited net down-regulation, consistent with the repressive function of SOX5 (Fig. 2f, Extended Data Fig. 6l, m).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“revealing strong concordance but a lower average fold change in the cerebellum.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Compared to this study, samples from ref. 4 were prepared by poly(A) selection RNA-seq, exhibit lower RNA integrity number (RIN, median 4.8 versus 7.3), have lower median sequencing depth (11 million versus 40 million), exhibit greater 5′−3′ bias, and have generally greater variability across all QC metrics.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
What the sources say
- Not checked yetcites [4] Gupta, S. et al. Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nat. Commun. 5, 5748 (2014) source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“ESRP2 is expressed but not significantly different between ASD and control cortex.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“PCR validation and sashimi plots for nine splicing events delineated in Extended Data Fig. 4d”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
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In the paper
“Module plot and GO term enrichment for CTX.M24, which is enriched in ASD-associated rare variants and lncRNAs.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Example of a strongly conserved lncRNA, which shows robust expression in all three species.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
boosted- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“ESRP1 is not expressed in cortex”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Approximately 85% of ASD samples are classified successfully around a false positive rate of 20%.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
What the sources say
- Not checked yetcites [8] Voineagu, I. et al. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474, 380–384 (2011) source
- Not checked yetcites [47] Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1–22 (2010) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“RT–PCR validation of the two lncRNAs shown in Fig. 1c, d; P values computed by two-sided Wilcoxon rank-sum test.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
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In the paper
“The first principal component of the cortex differential splicing set is strongly associated with diagnosis, but not other factors.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood1–3.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [1] Gaugler, T. et al. Most genetic risk for autism resides with common variation. Nat. Genet. 46, 881–885 (2014) source
- Not checked yetcites [2] Gratten, J., Visscher, P. M., Mowry, B. J. & Wray, N. R. Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease. Nat. Genet. 45, 234–238 (2013) source
- Not checked yetcites [3] de la Torre-Ubieta, L., Won, H., Stein, J. L. & Geschwind, D. H. Advancing the understanding of autism disease mechanisms through genetics. Nat. Med. 22, 345–361 (2016) source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“We confirmed that confounders do not account for the differential splicing signal, reproduced the global differential splicing signal with an alternative pipeline15, and performed technical validation with RT–PCR (Extended Data Figs 4d–g, 5a), confirming the differential splicing analysis.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [15] Wu, J., Anczuków, O., Krainer, A. R., Zhang, M. Q. & Zhang, C. OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res . 41, 5149–5163 (2013) source
boosted- Asserted: passes — The authors put it forward as true.
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In the paper
“Among the transcription factors identified, SOX5 was of particular interest because of its known role in mammalian corticogenesis23,24, its sole membership in the ACP set, and its correlation with predicted targets in the brains of control subjects, which is lost in ASD (Fig. 2b–d).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [23] Kwan, K. Y. et al. SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons. Proc. Natl Acad. Sci. USA 105, 16021–16026 (2008) source
- Not checked yetcites [24] Lamb, A. N. et al. Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features. Hum. Mutat. 33, 728–740 (2012) source
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
In the paper
“We demonstrated the robustness of attenuation in cortical patterning in ASD by confirming that the ACP set was not more variable than other genes, that attenuation of cortical patterning was robust to removal of previously analysed samples8, and that the effect could also be observed using a different classification approach (Extended Data Fig. 6b–h).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [8] Voineagu, I. et al. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474, 380–384 (2011) source
boosted- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This analysis corroborates and extends previous work by identifying sub-modules of those previously identified, thus demonstrating greater biological specificity (Extended Data Figs 8e, 9a).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Notably, the differential splicing molecular signature is not driven by DGE (Extended Data Fig. 4h), consistent with the observation that splicing alterations are related to common disease risk independently of gene expression changes16.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [16] Li, Y. I. et al. RNA splicing is a primary link between genetic variation and disease. Science 352, 600–604 (2016) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This DGE signal was consistent across methods, unrelated to major confounders, and found in more than two-thirds of ASD samples (Extended Data Fig. 1j–m).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Moreover, 20 of these lncRNAs have been shown to interact with microRNA (miRNA)–protein complexes, and 9 with the fragile X mental retardation protein (FMRP), whose mRNA targets are enriched in ASD risk genes9,10.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [9] Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014) source
- Not checked yetcites [10] Parikshak, N. N. et al. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 155, 1008–1021 (2013) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This overlap supports a model of ASD pathophysiology based on changes in the balance of excitation and inhibition and in neuronal activity22 and suggests that alterations in transcript structure are likely to be an important component.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [22] Mullins, C., Fishell, G. & Tsien, R. W. Unifying views of autism spectrum disorders: a consideration of autoregulatory feedback loops. Neuron 89, 1131–1156 (2016) source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Remarkably, CTX.M24 was significantly enriched for lncRNAs, genes expressed highly during fetal cortical development, and genes harbouring protein-disrupting mutations found in ASD, suggesting that lncRNAs will be important targets for investigation in ASD10,25 (FDR < 0.05, Extended Data Fig. 9a, g).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [10] Parikshak, N. N. et al. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 155, 1008–1021 (2013) source
- Not checked yetcites [25] Willsey, A. J. et al. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 997–1007 (2013) source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Together, the DGE and differential splicing analyses in dup15q provide further biological validation of the ASD transcriptomic signature and demonstrate that a genetically defined form of ASD exhibits similar changes to idiopathic ASD.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
boostedcorrelationaln = 9- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Notably, we used a modified version of WGCNA that involves bootstrapping the underlying dataset 100 times and constructing 100 networks. The consensus of these networks (median edge strength across all bootstrapped networks) was then used as the final network39, ensuring that a subset of samples does not drive the network structure.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Co-expression network analysis.
What the sources say
- Not checked yetcites [39] Langfelder, P. & Horvath, S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst. Biol. 1, 54 (2007) source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The sample dissections, RNA extractions, and RNA sequencing experiments were randomized (Supplementary Information).”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Brain tissue.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“In this regard, it is notable that the observed transcriptome changes are consistent with an ongoing process that is triggered largely by genetic and prenatal factors3,9,10,23, but that evolves during the first decade of brain development.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
What the sources say
- Not checked yetcites [3] de la Torre-Ubieta, L., Won, H., Stein, J. L. & Geschwind, D. H. Advancing the understanding of autism disease mechanisms through genetics. Nat. Med. 22, 345–361 (2016) source
- Not checked yetcites [9] Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014) source
- Not checked yetcites [10] Parikshak, N. N. et al. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 155, 1008–1021 (2013) source
- Not checked yetcites [23] Kwan, K. Y. et al. SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons. Proc. Natl Acad. Sci. USA 105, 16021–16026 (2008) source
hedgeddirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Similar to d except for the differential alternative splicing analysis.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
plain- Asserted: fails — The authors may not put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The authors may not put it forward as true. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“the known positive correlation between SRRM4 and RBFOX1 and anticorrelation between PTBP1 and SRRM4 (refs 14,19)”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Extended Data
What the sources say
- Not checked yetcites [14] Irimia, M. et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159, 1511–1523 (2014) source
- Not checked yetcites [19] Raj, B. et al. A global regulatory mechanism for activating an exon network required for neurogenesis. Mol. Cell 56, 90–103 (2014) source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“However, the correlation between the number of detected events in genes and gene length is minimal (R2 = 0.004), and the correlation is even smaller for events at P < 0.01 (R2 = 0.00012) demonstrating that longer genes are not more likely to contain differential splicing events.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Enrichment analysis of gene sets and common variation.
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The investigators were blinded to diagnosis until the analysis but unblinded during the analysis.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Brain tissue.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Co-expression of lncRNAs with genes harbouring ASD-associated protein coding mutations suggests that these noncoding RNAs are involved in similar biological functions and are potential candidate ASD risk loci.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > Abstract
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Notably, this sample size is underpowered to evaluate significant changes in many genes or splicing events; however, the goal was to validate the accuracy of our data and analyses across genes, so we show the correlation of fold changes between ASD and control across genes or events.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Quantitative real-time PCR validation.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“No statistical methods were used to predetermine sample size.”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Brain tissue.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper relies on this without support.
Post-mortem brain transcriptome measurements reflect the molecular pathology of ASD in living individuals.
“Here, through post-mortem genome-wide transcriptome analysis of the largest cohort of samples analysed so far, to our knowledge4–7, we interrogate the noncoding transcriptome, alternative splicing, and upstream molecular regulators to broaden our understanding of molecular convergence in ASD.”
The paper relies on this without support.
The control subjects are free of ASD and comparable to the ASD subjects in ways that do not confound the transcriptomic comparisons.
“We performed rRNA-depleted RNA sequencing (RNA-seq) of 251 post-mortem samples of frontal and temporal cortex and cerebellum from 48 individuals with ASD and 49 control subjects (Methods and Extended Data Fig. 1a–h).”
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“These DE genes exhibited substantial enrichment for known pathways and cell type specific markers derived from single nucleus RNA-Seq in human brain (Fig 1D-E) (21), consistent with previously observed patterns (1, 19).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“For decades, changes in microglial density, morphology, and transcriptional state have been observed in postmortem brain tissue of patients with neurological and psychiatric disorders17–21.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [21]
Experimental — accuracy not yet measuredIn the citing paper
“For example, ASD postmortem brains exhibit cell-type specific gene expression signatures such as upregulation of glial genes and downregulation of neuronal genes30.”
From A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles (2020) · cites this paper as [30]
In the citing paper
“In ASD, these analyses, replicated using different methods and samples, implicate synaptic and neuronal signaling pathways overlapping with other causal gene-based network methods (Parikshak et al., 2016; Voineagu et al., 2011).”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Parikshak et al., 2016
In the citing paper
“Data was generated across eight studies (2, 19, 20), uniformly processed, and combined through a consolidated genomic data processing pipeline ((21); Fig S1), yielding a total of 2188 samples passing quality control (QC) for this analysis, representing frontal and temporal cerebral cortex from 1695 unique subjects across the lifespan, including 279 technical replicates (Fig S2).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“and with previous RNA-Seq studies of individual disorders (ASD: ⍴=0.96, ref (19); SCZ ⍴=0.78, ref (2); SCZ ⍴=0.80, ref (24); BD ⍴=0.85, ref (1); Spearman ⍴ of log2FC, all P’s<10−16).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“We found significant overlap (42%, P=3.42×10−27; Fisher’s exact test) of the ASD DS intron clusters and splicing changes identified in a previous study (19) that used a different method and only a subset of the samples in our ASD and control cohorts (Table S3).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“Previous studies have identified alterations in local splicing events in ASD (19, 30) and in smaller cohorts in SCZ (2, 24) and BD (31).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“Multiple neuronal and synaptic signaling pathways have been previously demonstrated to be downregulated in a diminishing gradient across ASD, SCZ, and BD brains without identification of clear disease-specific signals for these neuronal-synaptic gene sets (1, 2, 16, 19, 56, 57).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“and both microglia and astrocytes in ASD (19, 70).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“although post-mortem microglial upregulation was observed only in ASD (1, 19, 70).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [19]
In the citing paper
“In humans, post-mortem genome-wide transcriptome analysis has revealed age-related changes in the trajectory of microglial and synaptic dysfunction that may reflect an early developmental alteration in microglial function163.”
From Microglial signatures and their role in health and disease (2018) · cites this paper as [163]
In the citing paper
“We observed an enrichment for variants associated with schizophrenia, but not for DEG found in ASD or SCZ postmortem brain tissue35,36.”
From Neuronal defects in a human cellular model of 22q11.2 deletion syndrome (2020) · cites this paper as [35]
In the citing paper
“The transcriptional program in ASD brains is distinct from that of TD brains (Gandal et al., 2018; Parikshak et al., 2016; Voineagu et al., 2011).”
From Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019) · cites this paper as Parikshak et al., 2016
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Co-expression network analysis.
“quartic splines”
§ Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism > METHODS > Co-expression network analysis.
“(degree = 2, span = 2/3)”
Citations
Cites
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“43 ) followed by multivariate analysis of transcript splicing, MATS 35 ) with PSI values obtained via another method (read alignment by OLego followed by PSI quantification with Quantas 15 ). g , Comparison of Δ PSI values between RT–PCR and RNA-seq for nine splicing events (Supplementary Table 3).…”
Biological insights from 108 schizophrenia-associated genetic loci
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“Disease GWAS studies evaluated include ASD 54 , schizophrenia 55 , inflammatory bowel disease 56 , type 2 diabetes mellitus 57 and serum lipid levels 58 .”
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
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Self-citationLD Score regression distinguishes confounding from polygenicity in genome-wide association studies
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Cited by
Sorted by citations
Identification of common genetic risk variants for autism spectrum disorder
Autism Spectrum Disorder Working Group of the Psychiatric Genomics Consortium, Grove, J., BUPGEN, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, 23andMe Research Team, Ripke, S., Als, T. D., Mattheisen, M., Walters, R. K., Won, H., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0344-8 · Cited by 2,421
Self-citationThe functions and unique features of long intergenic non-coding RNA
Ransohoff, J. D., Wei, Y., & Khavari, P. A. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.104 · Cited by 1,364
Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., et al. (2018) · Science · doi:10.1126/science.aat8127 · Cited by 1,247
“this signal from astrocyte and microglial populations (13, 19).”
InfluentialSelf-citationMicroglial signatures and their role in health and disease
Butovsky, O., & Weiner, H. L. (2018) · Nature Reviews Neuroscience · doi:10.1038/s41583-018-0057-5 · Cited by 1,046
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice
Sharon, G., Cruz, N. J., Kang, D.-W., Gandal, M. J., Wang, B., Kim, Y.-M., Zink, E. M., Casey, C. P., Taylor, B. C., Lane, C. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.05.004 · Cited by 1,182
“…brains exhibited differential patterns of alternative splicing (AS), a feature found in human ASD brains (Gandal et al., 2018; Irimia et al., 2014; Parikshak et al., 2016; Parras et al., 2018). rMATS analysis (Shen et al., 2014) identified 560 genes that showed different AS events between oASD and…”
BackgroundMethodInfluentialSelf-citation
Metadata
- Authors
- Parikshak, N. N., Swarup, V., Belgard, T. G., Irimia, M., Ramaswami, G., Gandal, M. J., Hartl, C., Leppa, V., Ubieta, L. D. L. T., Huang, J., Lowe, J. K., Blencowe, B. J., Horvath, S., & Geschwind, D. H.
- Affiliations
- University of California, Los Angeles (US)
- Universitat Pompeu Fabra (ES)
- University of Toronto (CA)
- Corresponding author
- Geschwind, Daniel H.
- ORCID
- Venue
- Nature
- Published
- 2016-12-05
- Volume
- 540
- Issue
- 7633
- Pages
- 423-427
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7102905
- OpenAlex
- W2560760305
- Semantic Scholar
- 16b7fc7c9c26dd8a077bd54c3c7ae75b50e9dc8d
- Cited by
- 685
- References
- 61
- Citations by year
- 2026: 45 · 2025: 54 · 2024: 65 · 2023: 57 · 2022: 75 · 2021: 94 · 2020: 113 · 2019: 83 · 2018: 61 · 2017: 34 · 2016: 3
- FWCI
- 38.40
- Type
- journal article
- Language
- en
- Update notices
- correction (2018-07-11)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Simons Foundation
- University of Toronto
- National Institutes of Health (5r01mh094714-04, MH060233)
- Canadian Institutes of Health Research
- National Institute of Mental Health (R01-MH094714, F30MH099886, R01MH100027, 5R01 MH09714, MH100027, T32MH073526, R37MH060233)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- autism spectrum disorder, long non-coding RNA, alternative splicing, SOX5, frontal and temporal cortex, microglial function, synaptic function, age-related gene expression, co-expression network, molecular convergence
- MeSH terms
- Autism Spectrum Disorder, Animals, Autopsy, Chromosome Aberrations, Chromosomes, Human, Pair 15, Exons, Frontal Lobe, Gene Expression Regulation, Humans, Intellectual Disability, Neurons, Primates, Species Specificity, Temporal Lobe, Genome, Human, Case-Control Studies, Alternative Splicing, Gene Expression Profiling, SOXD Transcription Factors, Transcriptome, RNA, Long Noncoding
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