mRNABench
Collection
Collection of datasets re-hosted for mRNABench: https://github.com/morrislab/mRNABench • 13 items • Updated • 3
Datasets:
gene stringlengths 2 10 | chromosome stringclasses 22
values | sequence stringlengths 100 12.3k | cds sequencelengths 100 12.3k | splice sequencelengths 100 12.3k | target float32 1.89 6.78 |
|---|---|---|---|---|---|
DPM1 | 20 | ATTCCGCTTCCGGCATCTGGCTCAGTTCCGCCATGGCCTCCTTGGAAGTCAGTCGTAGTCCTCGCAGGTCTCGGCGGGAGCTGGAAGTGCGCAGTCCACGACAGAACAAATATTCGGTGCTTTTACCTACCTACAACGAGCGCGAGAACCTGCCGCTCATCGTGTGGCTGCTGGTGAAAAGCTTCTCCGAGAGTGGAATCAACTATGAAATTATAATCATAGATGATGGAAGCCCAGATGGAACAAGGGATGTTGCTGAACAGTTGGAGAAGATCTATGGGTCAGACAGAATTCTTCTAAGACCACGAGAGAAAAAGTTG... | [
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SCYL3 | 1 | TGTCCCGTTTCCGGACCCGTCTCTATGGTGTAGGAGAAACCCGGCCCCCAGAAGATTGTGGGTGTAGTGGCCACAGCCTTACAGGCAGGCAGGGGTGGTTGGTGTCAACAGGGGGGCCAACAGGGTACCAGAGCCAAGACCCTCGGCCTCCTCCCCCGCCGCCTTCCTGCAGATCTGCTTGGCTTTGAGGAAGAGTGGCAGTACTGCCTCACTGCATAAGGGATGGGATCAGAGAACAGTGCTTTAAAGAGCTATACACTGAGAGAACCACCATTTACCTTACCCTCTGGACTTGCTGTTTATCCCGCTGTACTGCAAGA... | [
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0... | 3.337093 |
CFH | 1 | CTAGTTTCAACTTCCTTTTGCAGCAAGTTCTTTCCTGCACTAATCACAATTCTTGGAAGAGGAGAACTGGACGTTGTGAACAGAGTTAGCTGGTAAATGTCCTCTTAAAAGATCCAAAAAATGAGACTTCTAGCAAAGATTATTTGCCTTATGTTATGGGCTATTTGTGTAGCAGAAGATTGCAATGAACTTCCTCCAAGAAGAAATACAGAAATTCTGACAGGTTCCTGGTCTGACCAAACATATCCAGAAGGCACCCAGGCTATCTATAAATGCCGCCCTGGATATAGATCTCTTGGAAATGTAATAATGGTATGCAG... | [
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FUCA2 | 6 | GCGGCATACTCAGCGGCAGAGACGGAAGAACAGCGCTCCCGAGGCCGCGGGAGCCTGCAGAGAGGACAGCCGGCCTGCGCCGGGACATGCGGCCCCAGGAGCTCCCCAGGCTCGCGTTCCCGTTGCTGCTGTTGCTGTTGCTGCTGCTGCCGCCGCCGCCGTGCCCTGCCCACAGCGCCACGCGCTTCGACCCCACCTGGGAGTCCCTGGACGCCCGCCAGCTGCCCGCGTGGTTTGACCAGGCCAAGTTCGGCATCTTCATCCACTGGGGAGTGTTTTCCGTGCCCAGCTTCGGTAGCGAGTGGTTCTGGTGGTATTGG... | [
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FUCA2 | 6 | CAGCGCTCCCGAGGCCGCGGGAGCCTGCAGAGAGGACAGCCGGCCTGCGCCGGGACATGCGGCCCCAGGAGCTCCCCAGGCTCGCGTTCCCGTTGCTGCTGTTGCTGTTGCTGCTGCTGCCGCCGCCGCCGTGCCCTGCCCACAGCGCCACGCGCTTCGACCCCACCTGGGAGTCCCTGGACGCCCGCCAGCTGCCCGCGTGGTTTGACCAGGCCAAGTTCGGCATCTTCATCCACTGGGGAGTGTTTTCCGTGCCCAGCTTCGGTAGCGAGTGGTTCTGGTGGTATTGGCAAAAGGAAAAGATACCGAAGTATGTGGAA... | [
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GCLC | 6 | AGGAAGAAGCCAGTGCACCAGACCGGCAAAGAGAAGCGGGAGCCGCCGCGGCAGCGCGGCCGTGGGGTCCGCCGCCGCCGCATCGGAGCGGGAGGAGGAGCAGCGGGGAGGGCGAGGCCGCCGGGCCGAGAGCCGTCCCGCCTGCTCTCGGTCTTCTGCCTTCGCCTCCGCGCGGTGCGTCGGACCCAGGGTCTGTCACCTGGGCGCCAGGGGCCGCCGCCGGGGAGCCGGAGCGGGCAGGACCCTCCCTCCGCCGACTGCGGCCCGAGAGCGCCCCCGCGGGGTGGAGCGGCAGCCGCCTTCTGCGGGCGGCTGAGTGT... | [
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STPG1 | 1 | GGAGTTACCTCGCGGACGGCGGAAGGTGGACTCGCGAATGTTAGGCCTGTGGGTGCCATAGCGACCGGGAGGTTGGGCTGGCCAGATTCAGCTGCCGGGACCGGACCAGGTGCTTAGGAGAACATGCAGTAGAACTTTTCATCAAACAAATGGAACACGTCACAGAATTTTGCTAACATGGACAACTCTGCACAGAAAAATGAACGCACTGGCAAACATCCCAGACGTGCCAGTGAAGTACAGAAAGGTTTTACTGCTGCATATCCAACACAATCCTCCATTCCTTTTAAATCTCAAGCTTCAGTAATCCCAGAATCAGA... | [
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STPG1 | 1 | ATAGCGACCGGGAGGTTGGGCTGGCCAGATTCAGCTGCCGGGACCGGACCAGGTGCTTAGGAGAACATGCAGTAGAACTTTTCATCAAACAAATGGAACACGTCACAGAATTTTGCTAACATGGACAACTCTGCACAGAAAAATGAACGCACTGGCAAACATCCCAGACGTGCCAGTGAAGTACAGAAAGAATGATATCCCAGGACCTGGGTTCTACAATGTTATTCACCAGTCACCGGTGTCCAACAGTGTCTCATTGTCCAAGAAAGGAACTTGCATGTTTCCCTCAATGTGCGCCCGATTGGACACCATCATTTCTA... | [
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NIPAL3 | 1 | GAATTGGGAAGGGATGAAGGAGGCTGTGCCTCCGGGTTGCACGAAGAGTCCGAGTCATTTCTCAGAAGGTTTTGATAGGTGGGCCTTAGAGGAGACGCCGCCGAGCACCGCAAGAACTGGAAAACACACCCCTCTCTGTCTGCCTGGGAGAGCCACGGAAATTGGCACTTCTCTGAGTGAAGCTGAGGAGAAGGCTGTAAATCTGCCAAAACAGCCTTGAAGTATTCTTTTGTCATGAGGAAGTGACGGCTGCTGGAGGGAGGTGAACACCACAAGGAGAGATGGCATCTGGCCTGGGCCCCGCCTAGCAGCAGCTCCAC... | [
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NIPAL3 | 1 | ATTTCTCAGAAGGTTTTGATAGGTGGGCCTTAGAGGAGACGCCGCCGAGCACCGCAAGAACTGGAAAACACACCCCTCTCTGTCTGCCTGGGAGAGCCACGGAAATTGGCACTTCTCTGAGTGAAGCTGAGGAGAAGGCTGTAAATCTGCCAAAACAGCCTTGAAGTATTCTTTTGTCATGAGGAAGTGACGGCTGCTGGAGGGAGGTGAACACCACAAGGAGAGATGGCATCTGGCCTGGGCCCCGCCTAGCAGCAGCTCCACCTCCTAGGCCAGGCCCTGTGGGATGCGCCACTAGACCACCATGGACGGATCCCACA... | [
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ANKIB1 | 7 | GGGTCGGCGGCCGGGCTGCTGCCGTTCCTGCTCCTTTTCACTGGACCTGCAGTCTCTCAGGGGCTGGTGGCAGGCGACTAGGAGACTAGGGTGGTGGCGGTGGGGGTGCCAGCGGCTGAGCCGGAGCCGGAGCCGGAGGCGGGGGAGGGGAAGAGGGCGGCCGGGGCTGCGAGCGCGCAAGGCTGGAACATGAGCCGGGCTTGACCGCGAGGCGGAGGCAAGAGCCACCGCCCCCTCTTCCCCTCCCCCGAGTGAGGCGGCGCAGCGGCCGGAGAGGGATGGGGGGCGCCCACCCAGTCTGAGCCTCGCCGCGGGCGCCT... | [
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CYP51A1 | 7 | GGGACCCGAGGGGTGGGGCTGGGTTTAGTAGGAGACCTGGGGCAAGGCCCCCTGTGGACGACCATCTGCCAGCTTCTCTCGTTCCGTCGATTGGGAGGAGCGGTGGCGACCTCGGCCTTCAGTGTTTCCGACGGAGTGAATGGCGGCGGCGGCTGGGATGCTGCTGCTGGGCTTGCTGCAGGCGGGTGGGTCGGTGCTGGGCCAGGCGATGGAGAAGGTGACAGGCGGCAACCTCTTGTCCATGCTGCTGATCGCCTGCGCCTTCACCCTCAGCCTGGTCTACCTGATCCGTCTGGCCGCCGGCCACCTGGTCCAGCTGC... | [
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KRIT1 | 7 | AAAGGGTGTGAACCCGGAAGCGATTTCATAGCCACGGTTTTTGGCTTTCATCGCTTTTTCTACATGTTTTTAGCCTCACCAGAAGTCTTTCATCTCGGTGGTCCAACTCAGGATCTCAGCCTCATTATTTTCTTACCCTTCTGGAGTGCATATGTGCCTTTACAGTTTCTGTTTGCAAACGCTGTCTAGCATACTAAGAGGATGTTAGCAAACCTGTTCCATGGACACTAAATGGCAGTTGTACATCTCCCCTCATCAGTCATAGTGACAACCAGAAATGCCCTCCATATTTTCCAGTGATCCCAGCAATGGGAAATCCA... | [
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LAP3 | 4 | GTGCTCGCTGGAGGGCGGTGCGAGGGGCCGAGCCGACAAGATGTTCTTGCTGCCTCTTCCGGCTGCGGGGCGAGTAGTCGTCCGACGTCTGGCCGTGAGACGTTTCGGGAGCCGGAGTCTCTCCACCGCAGACATGACGAAGGGCCTTGTTTTAGGAATCTATTCCAAAGAAAAAGAAGATGATGTGCCACAGTTCACAAGTGCAGGAGAGAATTTTGATAAATTGTTAGCTGGAAAGCTGAGAGAGACTTTGAACATATCTGGACCACCTCTGAAGGCAGGGAAGACTCGAACCTTTTATGGTCTGCATCAGGTATGAG... | [
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LAP3 | 4 | GCCGAGCCGACAAGATGTTCTTGCTGCCTCTTCCGGCTGCGGGGCGAGTAGTCGTCCGACGTCTGGCCGTGAGACGTTTCGGGAGCCGGAGTCTCTCCACCGCAGACATGACGAAGGGCCTTGTTTTAGGAATCTATTCCAAAGAAAAAGAAGATGATGTGCCACAGTTCACAAGTGCAGGAGAGAATTTTGATAAATTGTTAGCTGGAAAGCTGAGAGAGACTTTGAACATATCTGGACCACCTCTGAAGGCAGGGAAGACTCGAACCTTTTATGGTCTGCATCAGGACTTCCCCAGCGTGGTGCTAGTTGGCCTCGGC... | [
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LAP3 | 4 | GCGAGTAGTCGTCCGACGTCTGGCCGTGAGACGTTTCGGGAGCCGGAGTCTCTCCACCGCAGACATGACGAAGGGCCTTGTTTTAGGAATCTATTCCAAAGAAAAAGAAGATGATGTGCCACAGTTCACAAGTGCAGGAGAGAATTTTGATAAATTGTTAGCTGGAAAGCTGAGAGAGACTTTGAACATATCTGGACCACCTCTGAAGGCAGGGAAGACTCGAACCTTTTATGGTCTGCATCAGGACTTCCCCAGCGTGGTGCTAGTTGGCCTCGGCAAAAAGGCAGCTGGAATCGACGAACAGGAAAACTGGCATGAAG... | [
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LAP3 | 4 | GAGTAGTCGTCCGACGTCTGGCCGTGAGACGTTTCGGGAGCCGGAGTCTCTCCACCGCAGACATGACGAAGGGCCTTGTTTTAGGAATCTATTCCAAAGAAAAAGAAGATGATGTGCCACAGTTCACAAGTGCAGGAGAGAATTTTGATAAATTGTTAGCTGGAAAGCTGAGAGAGACTTTGAACATATCTGGACCACCTCTGAAGGCAGGGAAGACTCGAACCTTTTATGGTCTGCATCAGCGGGGTGCAGGCAGATTCAAGACCTGGAGCTCTCGTCTGTGGAGGTGGATCCCTGTGGAGACGCTCAGGCTGCTGCGG... | [
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End of preview. Expand in Data Studio
Overview
Mean Ribosome Load (MRL) measures the mean number of ribosomes attached to a given transcript. This dataset is collected from Sugimoto and Ratcliffe 2022, where MRL measurements are made in human kidney cancer cells. Importantly, this dataset is isoform-resolved, providing measurements at an isoform level.
This dataset is redistributed as part of mRNABench: https://github.com/morrislab/mRNABench
Data Format
Description of data columns:
target: Mean ribosome load for transcript.cds: Binary track which reports position of first nucleotide in each codon in CDS.splice: Binary track which reports position of the 3' end of each exon, indicating splice sites.
Data Source
This dataset is generated using the data collected in Sugimoto and Ratcliffe 2022, which is licensed under the Creative Commons Attribution 4.0 International License.
Original paper: https://www.nature.com/articles/s41594-022-00819-2
Original dataset source: https://www.nature.com/articles/s41594-022-00819-2#Sec63
Citation: Sugimoto, Y. & Ratcliffe, P. J. Isoform-resolved mRNA profiling of ribosome
load defines interplay of HIF and mTOR dysregulation in kidney cancer. Nature
Structural Molecular Biology 29, 871–880 (2022).
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