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Data Sets |
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| Species | Description | File Name | Contact |
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RNA-Seq Data Sets |
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| H.sap-C.ele-D.mel | RNA-seq datasets used in comparative analysis | Comparative_Datasets.xlsx | Carrie Davis, CSHL |
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Protein-Coding Gene Annotation |
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| H.sapiens | Gencode 10 protein-coding genes | gen10_CDS+exons_only_protein-coding_only.gtf.gz | Julien Lagarde, CRG Barcelona |
| C.elegans | modENCODE June 2012 freeze protein-coding genes | AG1201.integrated_transcripts_strictly_coding.ws220.gtf.gz | LaDeana Hillier, Washington U St. Louis |
| D.melanogaster | modENCODE June 2012 freeze protein-coding genes | coding_Celniker_Drosophila_Annotation_20120616_1428.gtf.gz | Ben Brown, UC Berkeley |
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Human-Worm-Fly Ortholog Lists |
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| H.sap-C.ele-D.mel | eMIT Human-Worm-Fly Orthologs | Modencode.merged.orth20120611_wfh_comm_all.csv | Daifeng Wang Yale / Kellis Lab MIT |
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All Features and Processed Values of Genes |
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| H.sapiens | Human coding gene features and values | human_gene.xlsx | Gang Fang, Yale |
| C.elegans | Worm coding gene features and values | worm_gene.xlsx | Gang Fang, Yale |
| D.melanogaster | Fly coding gene features and values | fly_gene.xlsx | Gang Fang, Yale |
Pseudogenes |
| H.sapiens | Pseudogenes GENCODE v10 | HumanPseudogenes.bed | Mark Gerstein / Cristina Sisu, Yale |
| C.elegans | Pseudogenes WS220 | WormPseudogenes.bed | Mark Gerstein / Cristina Sisu, Yale |
| D.melanogaster | Pseudogenes FlyBase 5.45 | FlyPseudogenes.bed | Mark Gerstein / Cristina Sisu, Yale |
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Statistics of pseudogenes |
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| H.sapiens | psiDR | Human-psiDR.bed | Cristina Sisu, Yale |
| C.elegans | psiDR | Worm-psiDR.bed | Cristina Sisu, Yale |
| D.melanogaster | psiDR | Fly-psiDR.bed | Cristina Sisu, Yale |
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Orthologs-Pseudogenes |
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| H.sap-C.ele-D.mel | Pseudogene from 1-1-1 gene orthologs | Ortholog-1-1-1-HWF-Pseudogenes.txt | Cristina Sisu, Yale |
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Pfam-Pseudogenes |
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| H.sap-C.ele-D.mel | PFAM family distribution of pseudogenes | PFAM-familyDistribution-Pseudogenes.txt | Cristina Sisu, Yale |
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TARs |
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| H.sapiens | Stringent Human TAR list Feb 6, 2013 | human_exon_disc_90_tars_02_06_2013.bed | Arif Harmanci / Joel Rozowsky, Yale |
| C.elegans | Stringent Worm TAR list Feb 6, 2013 | worm_exon_disc_90_tars_02_06_2013.bed | Arif Harmanci / Joel Rozowsky, Yale |
| D.melanogaster | Stringent Fly TAR list Feb 6, 2013 | fly_exon_disc_90_tars_02_06_2013.bed | Arif Harmanci / Joel Rozowsky, Yale |
| H.sapiens | Relaxed Human TAR list Feb 6, 2013 | human_exon_disc_98_tars_02_06_2013.bed | Arif Harmanci / Joel Rozowsky, Yale |
| C.elegans | Relaxed Worm TAR list Feb 6, 2013 | worm_exon_disc_98_tars_02_06_2013.bed | Arif Harmanci / Joel Rozowsky, Yale |
| D.melanogaster | Relaxed Fly TAR list Feb 6, 2013 | fly_exon_disc_98_tars_02_06_2013.bed | Arif Harmanci / Joel Rozowsky, Yale |
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Supervised ncRNA Predictions (novel ncRNA fragments) |
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| H.sapiens | Human supervised ncRNA predictions Feb 6 , 2013 | hg ncRNA predictions 6Feb13.bed | John Lu / Arif Harmanci / Joel Rozowsky, Yale |
| C.elegans | Worm supervised ncRNA preditions Feb 6, 2013 | ce ncRNA predictions 6Feb13.bed | John Lu / Arif Harmanci / Joel Rozowsky, Yale |
| D.melanogaster | Fly supervised ncRNA predicitons Feb 6, 2013 | dm ncRNA predictions 6Feb13.bed | John Lu / Arif Harmanci / Joel Rozowsky, Yale |
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Fly strict non-coding gene |
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| D.melanogaster | modENCODE June 2012 freeze | strict_noncoding_Celniker_Drosophila_Annotation_20120616_1428.gtf | Ben Brown, UC Berkeley |
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Comparable and non-comparable non-coding RNA annotations |
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| H.sapiens | Human comparable ncRNA | human_consensus_ncRNAs_03_23_2013.gtf.tar.bz2 | Arif Harmanci, Yale |
| H.sapiens | Human non-comparable ncRNA | human_non_consensus_ncRNAs_03_23_2013.gtf.tar.bz2 | Arif Harmanci, Yale |
| C.elegans | Worm comparable ncRNA | worm_consensus_ncRNAs_03_23_2013.gtf.tar.bz2 | Arif Harmanci, Yale |
| C.elegans | Worm non-comparable ncRNA | worm_non_consensus_ncRNAs_03_23_2013.gtf.tar.bz2 | Arif Harmanci, Yale |
| D.melanogaster | Fly comparable ncRNA | fly_consensus_ncRNAs_03_23_2013.gtf.tar.bz2 | Arif Harmanci, Yale |
| D.melanogaster | Fly non-comparable ncRNA | fly_non_consensus_ncRNAs_03_23_2013.gtf.tar.bz2 | Arif Harmanci, Yale |
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Antisense Transcription |
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| H.sapiens | List of sense-antisense pairs in Human | human_antisense.pairs.txt | Ben Brown, UC Berkeley |
| C.elegans | List of sense-antisense pairs in Worm | worm_antisense.pairs.txt | Ben Brown, UC Berkeley |
| D.melanogaster | List of sense-antisense pairs in Fly | fly_antisense.pairs.txt | Ben Brown, UC Berkeley |
| H.sap-C.ele-D.mel | -Counts of positionally conserved antisense RNAs in 3 species | positionally_equiv_antisense_counts.txt | Ben Brown, UC Berkeley |
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"Hourglass" modules and associated ncRNAs |
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| H.sap-C.ele-D.mel | Gene composition in 16 modules | HG_module.tar.gz | Daifeng Wang / Gang Fang, Yale |
| H.sap-C.ele-D.mel | ncRNA and TARs associated with the 16 modules | HG_module_ncRNA.tar.gz | Daifeng Wang / Gang Fang, Yale |