Down regulated genes from fibrolbasts of AGO2 mutation patients compared to age-matched individuals
Description:
ARGONAUTE-2 (AGO2) and associated miRNAs form the RNA-induced silencing complex (RISC), that targets mRNAs for translational silencing and degradation, as part of the RNA interference pathway. RNA sequencing was performed of primary dermal fibroblasts obtained from two patients bearing the p.L192P (cases 2 and 3) and one patient with the p.A367P mutation (case 14). The researchers compared the expression patterns of the protein coding transcripts to fibroblasts from age-matched individuals, who were either unaffected or bear a causative mutation unrelated to AGO2. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Down regulated genes were annotated as Ensembl gene ids. SRA Study id SRP233483. Cell Line Ontology CLO:0037302; Primary Human Dermal Fibroblasts.
Authors:
Davor Lessel, Daniela M Zeitler, Margot R F Reijnders, Andriy Kazantsev, Fatemeh Hassani Nia, Alexander Bartholomäus, Victoria Martens, Astrid Bruckmann, Veronika Graus, Allyn McConkie-Rosell, Marie McDonald, Bernarda Lozic, Ee-Shien Tan, Erica Gerkes, Jessika Johannsen, Jonas Denecke, Aida Telegrafi, Evelien Zonneveld-Huijssoon, Henny H Lemmink, Breana W M Cham, Tanja Kovacevic, Linda Ramsdell, Kimberly Foss, Diana Le Duc, Diana Mitter, Steffen Syrbe, Andreas Merkenschlager, Margje Sinnema, Bianca Panis, Joanna Lazier, Matthew Osmond, Taila Hartley, Jeremie Mortreux, Tiffany Busa, Chantal Missirian, Pankaj Prasun, Sabine Lüttgen, Ilaria Mannucci, Ivana Lessel, Claudia Schob, Stefan Kindler, John Pappas, Rachel Rabin, Marjolein Willemsen, Thatjana Gardeitchik, Katharina Löhner, Patrick Rump, Kerith-Rae Dias, Carey-Anne Evans, Peter Ian Andrews, Tony Roscioli, Han G Brunner, Chieko Chijiwa, M E Suzanne Lewis, Rami Abou Jamra, David A Dyment, Kym M Boycott, Alexander P A Stegmann, Christian Kubisch, Ene-Choo Tan, Ghayda M Mirzaa, Kirsty McWalter, Tjitske Kleefstra, Rolph Pfundt, Zoya Ignatova, Gunter Meister, Hans-Jürgen Kreienkamp
Up regulated genes from fibrolbasts of AGO2 mutation patients compared to age-matched individuals
Description:
ARGONAUTE-2 (AGO2) and associated miRNAs form the RNA-induced silencing complex (RISC), that targets mRNAs for translational silencing and degradation, as part of the RNA interference pathway. RNA sequencing was performed of primary dermal fibroblasts obtained from two patients bearing the p.L192P (cases 2 and 3) and one patient with the p.A367P mutation (case 14). The researchers compared the expression patterns of the protein coding transcripts to fibroblasts from age-matched individuals, who were either unaffected or bear a causative mutation unrelated to AGO2. Expression values were calculated by the method detailed in 'HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis' (Genome Biol. 2020, PMID: 32660516), and log base 2 of the fold change are presented with a FDR of <0.05. Up regulated genes were annotated as Ensembl gene ids. SRA Study id SRP233483. Cell Line Ontology CLO:0037302; Primary Human Dermal Fibroblasts.
Authors:
Davor Lessel, Daniela M Zeitler, Margot R F Reijnders, Andriy Kazantsev, Fatemeh Hassani Nia, Alexander Bartholomäus, Victoria Martens, Astrid Bruckmann, Veronika Graus, Allyn McConkie-Rosell, Marie McDonald, Bernarda Lozic, Ee-Shien Tan, Erica Gerkes, Jessika Johannsen, Jonas Denecke, Aida Telegrafi, Evelien Zonneveld-Huijssoon, Henny H Lemmink, Breana W M Cham, Tanja Kovacevic, Linda Ramsdell, Kimberly Foss, Diana Le Duc, Diana Mitter, Steffen Syrbe, Andreas Merkenschlager, Margje Sinnema, Bianca Panis, Joanna Lazier, Matthew Osmond, Taila Hartley, Jeremie Mortreux, Tiffany Busa, Chantal Missirian, Pankaj Prasun, Sabine Lüttgen, Ilaria Mannucci, Ivana Lessel, Claudia Schob, Stefan Kindler, John Pappas, Rachel Rabin, Marjolein Willemsen, Thatjana Gardeitchik, Katharina Löhner, Patrick Rump, Kerith-Rae Dias, Carey-Anne Evans, Peter Ian Andrews, Tony Roscioli, Han G Brunner, Chieko Chijiwa, M E Suzanne Lewis, Rami Abou Jamra, David A Dyment, Kym M Boycott, Alexander P A Stegmann, Christian Kubisch, Ene-Choo Tan, Ghayda M Mirzaa, Kirsty McWalter, Tjitske Kleefstra, Rolph Pfundt, Zoya Ignatova, Gunter Meister, Hans-Jürgen Kreienkamp
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "RISC-loading complex", which is defined as "A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "RISC-loading complex", which is defined as "A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "RISC-loading complex", which is defined as "A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Positional candidates for ZM_LATENCY measured in BXD RI Males & Females. ZM_LATENCY measures the latency to enter an open quadrant under the domain Basal Behavior.The QTL found on Chr 15 is a Suggestive QTL and spans 73 Mb to 79 Mb.
Neocortex Gene Expression Correlates for HARGREAVES_MEANBOTH measured in BXD RI Females obtained using GeneNetwork Neocortex ILM6v1.1 (Feb08) RankInv. The HARGREAVES_MEANBOTH measures Thermal Nociception Hargreaves' Test under the domain Pain. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for LD_DARK_DIST measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LD_DARK_DIST measures Light Dark Box Total distance traveled in dark compartment under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for LM_CUE_ACTIVITY measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_CUE_ACTIVITY measures Activity in altered context during presentation of cue under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for LM_PS_INTVL2 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_PS_INTVL2 measures Activity in 30 second interval post 2nd tone shock pairing under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for ZM_ACTIVITY measured in BXD RI Females & Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The ZM_ACTIVITY measures Zero Maze - Total Activity count; number of beam breaks under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for LM_PAIR1 measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The LM_PAIR1 measures Activity during 1st tone shock pairing under the domain Basal Behavior. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
A list of genes whose transcript abundance in the PFC changed significantly 4 hours after an acute dose of ethanol (1.8 g/kg). This list was generated using Fisher's Combined Probability test to analyze saline vs ethanol S-scores across B6 and D2 inbred strains (n=3) and 27 BXD RI lines (n=1). Statistical significance was determined using 1,000 permutations of S-score data and selecting for probe-sets with q-values < 0.05. Aaron Wolen 5-26-10.
Authors:
Wolen AR, Phillips CA, Langston MA, Putman AH, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF
cocaine related behavior 14 (Cocrb14) spans 43.765096 - 93.765096 Mbp (NCBI Build 37) on Chr 15. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
cocaine related behavior 15 (Cocrb15) spans 70.807693 - 120.807693 Mbp (NCBI Build 37) on Chr 15. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
QTL for ethanol withdrawal on Chr15 at D15Ncvs19 (0.00 Mbp , Build 37)
Description:
ethanol withdrawal spans 0.00 - 25.00 Mbp (NCBI Build 37) on Chr15. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for high-dose ethanol actions on Chr15 at D15Mit12 (12.77 Mbp , Build 37)
Description:
high-dose ethanol actions spans 0.00 - 37.77 Mbp (NCBI Build 37) on Chr15. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
Erwin VG, Markel PD, Johnson TE, Gehle VM, Jones BC
QTL for alcohol acceptance on Chr15 at D15Mit60 (57.48 Mbp , Build 37)
Description:
alcohol acceptance spans 32.48 - 82.48 Mbp (NCBI Build 37) on Chr15. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
McClearn GE, Tarantino LM, Rodriguez LA, Jones BC, Blizard DA, Plomin R
QTL for cocaine related behavior on Chr15 at D15Mit3 (83.88 Mbp , Build 37)
Description:
cocaine related behavior spans 58.88 - 108.88 Mbp (NCBI Build 37) on Chr15. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for alcohol consumption on Chr15 at D15Mit105 (87.33 Mbp , Build 37)
Description:
alcohol consumption spans 62.33 - 112.33 Mbp (NCBI Build 37) on Chr15. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
Vadasz C, Saito M, Gyetvai B, Mikics E, Vadasz C 2nd
QTL for cocaine induced activation on Chr15 at NA (92.79 Mbp , Build 37)
Description:
cocaine induced activation spans 67.79 - 117.79 Mbp (NCBI Build 37) on Chr15. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
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