Satellite papers

SUBMISSION PAGE

Looking for the satellite submission page-> go here https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Satellite_submission

Looking for phase 2 satellite submission page-> go here https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Time-courses_Satellite_papers

Time-courses Satellite papers

There is a separate page for the Time-courses_Satellite_papers.

Updated during Koyo meeting

Journal preferences survey and classification Media:Target_journal_preferences_aug17_master.xls

Instructions

Below you can find the list of satellite paper proposals collected in the February meeting. Please add the following information to each of the proposals

• Check the title
• provide brief outline of the proposal
• add/remove your name in case you are interested to work on this satellite paper

Proposal for satellites papers 2/25/2011 Purpose: list up potential satellites; avoid redundancies, make better papers Figure out potential titles to discuss how to negotiate with specific journals.

Add a set of sentences (mini abstract) on the wiki and write an abstract

Bioinformatics analysis methods

Normalization and clustering issues

• Outline: bla
• Group members: Tom Freeman

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Modulation of gene expression (Jess Mar)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Expanding transcriptional reg. networks (Vlad)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Tag clustering in helicos CAGE (Cesare)

• Outline:
• Group members: C. Furlanello, M. Chierici, D. Albanese, M. Roncador

1. Interested in including in special issue: Y

2. Appropriate journal for this article:Genome Research / Plos Comp Biol

3. Estimated month of submission: Feb 2012

Computational methods for networks comparisons (cesare)

• Outline: bla
• Group members: FBK (C. Furlanello, G: Jurman, ...) 

1. Interested in including in special issue: Y

2. Appropriate journal for this article:Genome Research / Plos Comp Biol

3. Estimated month of submission: Feb 2012

4. Class: Networks / Bioinformatics analysis methods

Tool to make the promoter subsets at will (do not ask us datasets!) (Albin)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Delve tag mapping paper (Timo L)

• Outline: Methods paper on Delve: a probabilistic read mapper.
• Group members: Timo Lassmann, Carsten Daub

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Classification of CAGE peaks (Timo L)

• Outline: Deeply sequenced CAGE libraries capture signals on many non-promoter regions. The purpose of this paper is to describe a strategy to separate TSS from non-TSS CAGE peaks (see: Media:CAGE_classification.pdf). Preliminary work suggest that further sub-classicifation of promoters based on the shape of the CAGE signal is possible (see: Media:Brood_october_2010.pdf).
• Group members: Timo Lassmann, Ben Brown, Colin Semple

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

"Comparing Clustering of hCAGE peaks" (Peak finder-noise elimination contest paper) (all runners)

• Outline: (may be merged with tag clustering in hCAGE) This manuscript will review the general
• Group members: ..., FBK, ...

1. Interested in including in special issue: Y

2. Appropriate journal for this article:Genome Research / Plos Comp Biol

3. Estimated month of submission: Jan 2011

4. Class: Bioinformatics analysis methods

A framework for assessment of cell-type specializations, divergences and identities (Albin)

• Outline: We aim to develop a methodological framework for describing transcriptional diversity in terms of cell-type specializations and divergences between individual and functionally related clades of cell types. This will, to a large extent, be based on information theory. Using a dimensionality-reduction approach inspired by bootstrap-like clustering we aim to infer the minimal set of promoters that describe cell-type identities. Rather than random selection of an increasing number of TCs (in a bootstrap manner), cluster stability indices will be calculated using an increasing number of TCs selected from the ranks of TCs according to contribution to overall divergences. This methodological framework may be used in a descriptive study but will also be essential for two additional satellite papers in which we will study enhancer-promoter associations and pre-initiation complex variability both with a focus on cell-type specific (biased) promoter usage.
• Group members: Robin Andersson, Albin Sandelin

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Mogrify: Predicting factors for cell conversion (Owen, Julian)

• Outline: We now know that cellular state is a plastic phenomenon which it is possible to control. There has been a number of reports in the literature where cells have been made to go from fully differentiated cell types to pluripotency and also from one fully differentiated cell type to another. Each of these experiments was guided by a process of trial and error in order to discover the transcription factors that were capable of inducing this reprogramming. This work presents a new network based method “Mogrify” for the identification of likely candidate transcription factors for cell reprogramming. We show that we are able to predict the known reprogramming factors for 3 successful trans-differentiations (heart, neuron and liver) and then provide evidence for a further as yet un-tested transdifferentiations. The technique is then run without human intervention on every combination of cell types in the FANTOM 5 set providing a list of likely reprogramming factors (with scores) for any transition, plus a resulting evaluation of potentially viable trans-differentiations. This is what we refer to as the reprogramming landscape, and whilst it is likely that not each of the sets would work it is the first step towards a true map of cell to cell transitions.

1. Interested in including in special issue: Y

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: draft available now

Genomics-broad scale analysis

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Common alternative TSS in cancer stem cells and development (Win Hide)

• Outline:
• Group members:Rama Sompallae, Emmanuel Dimont, Shannan Ho Sui, Oliver Hoffman and hopefully Boris' group.

1. Interested in including in special issue: Y

2. Appropriate journal for this article:Genome Research, PLoS Genetics

3. Estimated month of submission: Jan/Feb 2012

Impact of alternative promoters on biology of genes (Albin)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

How much do we need to sequence? Complexity of the transcriptome (Albin)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Revised analysis of zinc finger proteins (Tim Ravasi, David Hume)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Identification of distal regulation elements: role of enhancers in differentiation (Carsten, Boris, Ana P, Jose, YH)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

miRNA promoters (Hideya K, Eivind Al, )

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

CAGE tags on Pigs: Gain and loss of promoters (David Hume) [satellite of the pig genome]

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Regulatory transcription outside canonical promoters (Boris)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Transcription initiation in embryo development (Boris)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Promoters with multiple TSS configuration-multiple ways to use the same promoters (Boris, Kawaji)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Link Fantom 5 to genetic datasets (Peter Heutink; Juha K)

• Outline: Genome Wide Association Studies (GWAS) have been very succesfull in identifying new risk loci for multifactorial human disease. It has however been very difficult to identify the true biologically relevant variant. GWAS studies in general do not directly test the unknown causal variant but a variant that is in Linkage Disequilibrium with the causal variant. Studies to identify the causal variants are complicated by the observation that most signals from GWAS studies point to non-coding regions of the genome for which the functions are currently unknown. The dataset generated by FANTOM5 now allows to investigate the regions around the association signal for functional elements involved in transcription.

Research method: We have developed a statistical method to delineate the critical region for GWAS loci (Bochdanovits et al. Submitted). We aim to use this method on all publically available GWAS datasets in order to obtain the boundaries of identified GWAS loci. We will then superinpose these genomic region on FANTOM5 data from relevant tissues/celltypes for the disease and identify possible promoters. By using data from the 1000 Genomes project we will investigate if genomic variation exists in the identified promoters. These variants can then be tested for functional effects in cellular reporter assays.

• Group members: Peter Heutink, Juha Kere, Zoltan Bochdanovits and ......please sign up if you are interested.
  

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

DNA methylation affects TF binding and transcription (Yulia)

• Outline: It's commonly accepted that DNA methylation of a promoter repress transcription of this gene in normal tissues. Recently, a class of actively expressed genes having relatively methylated promoters has been discovered. The purpose of this research is to explore the idea that DNA methylation affects CG-rich TFBS, preventing some TF from binding to DNA, and therefore represses transcription.

• Details: DNA_methylation_and_transcription

• Group members: Yulia Medvedeva

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Comparison of different types/feature of promoters and genome features to study specific differences (Yulia)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Multiple genomics analysis on multiple datasets (Haru) Extension of the validation?

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Convergent evolution of retrotransposon promoters (Geoff)

• Outline: Following the model for the anti-apoptosis gene NAIP (Romanish et al., PLoS Genetics, 2007), we will start by screening the mouse and human genomes for instances where two different retrotransposons occupy the same or similar location in protein-coding genes (e.g. an Alu in human, a B2 in mouse). If this happens frequently enough to be interesting, we will overlay the F5 data onto the "convergent" retrotransposons to see how many are transcribed, what role they may have in regulation (e.g. Lunyak et al., Science, 2007) and if the events are more common for some pathways than others (e.g. in embryogenesis or brain development).
  
• Group members: Geoff, Piero
  

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Improving MARA analysis in a model of enhancer/promoter expressions (Saeed Omidi + Piotr)

• Outline: In this study, we aim to pinpoint the role of enhancers in expression variations across different cell/tissue-types. First, we need to identify enhancers, considering both CAGE data and enhancer predictive marks such as H3K4me1 and co-factor P300. Subsequently, by predicting TF binding sites within these regions, we will be enabled to plug this information into MARA and see whether it improves the fit to promoter expression.
  

• Group members: Saeed Omidi, Piotr Balwierz, Erik van Nimwegen

1. Interested in including in special issue: Y

2. Appropriate journal for this article:Genome Research or PLoS Computational Biology

3. Estimated month of submission: April 2012

Alternative TSS and alternative splicing (Nicolas)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Chimaeric RNA and 3D structure (if it works) (Nicolas)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Annotation of genes involved in biochemical, metabolic processes and signature for processes-for instance signature for tumors – expression based GO terms (Tom Freeman) (Richard Baldarelli, Jackson and GO groups) (David Hume)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Enhancer-promoter associations (Albin)

• Outline: We have observed that hCAGE captures transcribed enhancers and would like to study the specificity of enhancer usages across FANTOM5 samples with an ENCODE cell lines focus. Through similarities (low divergence) of usage patterns with GENCODE promoters, we aim at predicting promoter-enhancer associations. We will validate inferred associations (interactions) using Hi-C data for K562 and hopefully also through targeted 3C experiments. We would also like to study the dynamics of enhancer activity on predicted (and Hi-C supported) associated promoters. The K562 hemin time course will be particularly interesting to study.
• Group members: Robin Andersson, Eivind Valen, Albin Sandelin

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Systematic analysis of transcription start sites in avian development (chicken CAGE) (Guojun Sheng)

• Outline: Genome wide analysis of chicken TSSs.

• Group members: Marina Lizio2,4,*, Ruslan Deviatiiarov3,*, Hiroki Nagai1,*, Laura Galan6, Erik Arner2,4, Masayoshi Itoh2,4,5, Timo Lassmann2,4, Takeya Kasukawa2, Akira Hasegawa2, Marian Ros6, Yoshihide Hayashizaki4,5, Piero Carninci2,4, Alistair R. R. Forrest2,4,7, Hideya Kawaji2,4,5,#, Oleg Gusev2,3,5,8,# and Guojun Sheng1,9,#

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: May/2017

Blood group: fill in the holes, more discussion

Granulopoiesis analysis (Andreas Lenn.+Erik Arner)

• Outline:
• Group members: Andreas Lennartsson, Erik Arner

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Erythropoiesis (Peter K)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

HSC (Sugiyama san)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Macrophages (DH)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Subpopulations T cells and monocytes (Michael R)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Brain groups 4 papers Other priority areas in brain: discuss other brain and diseases (YH)

Evolution gene expression in vertebrates Martin + Peter Heutink

• Outline: Study the evolution of gene expression combining insights from each of the following:
  • Gene/transcript level changes in expression (and estimating it's constraint/diversification).
  • TSS/promoter turnover: orthologous genes using non-orthologous promoters, or changes in promoter-preference for one cell type between species.
  • Sequence evolution of core promoters and distant regulatory blocks correlated with changes in gene expression.
• Focus of the paper on the well matched cells between ((Human, (Macaque?)),(Mouse, Rat),Dog),Chicken) for which we have hCAGE data. (Cell types: Hepatocytes, Aortic smooth muscle cells, mesenchymal stem cells).
• Group members: Martin Taylor, Peter Heutink, Alison Meynert
• Details: Evolution in gene expression.

1. Interested in including in special issue: Y

2. Appropriate journal for this article:(Nature Genetics / Genome Research / Genome Biology / PLoS Genetics)

3. Estimated month of submission: Jan 2012

Transcriptional constrains seq evolution [Martin+Michiel talk]

• Outline: [Michiel:] Network analysis across organisms & evolution of regulatory networks, in particular of developmental networks. Are there any subnetworks particularly conserved between organisms? What does this tell us about the functional importance and relevance of specific subnetworks? Do we see any recurring patterns in the network (Uri Alon-type feed-forward loops)? What are the conservation patterns and rates of divergence of transcription factors and specific regulatory relations? Do we see turnover of TFBSs, or do we see conservation of TFBSs in alignments? This can be applied specifically to brain, or more generally to all CAGE samples. TFBS prediction in Neanderthal compared to Homo sapiens would be really cool.
• Group members: Martin, Michiel, Peter Heutink
• Martin's and Michiel's idea for this paper may overlap or may be complementary to each other; we need to discuss this. This may end up as two satellite papers or one integrated one.

1. Interested in including in special issue: Y

2. Appropriate journal for this article:(Genome Research / Genome Biology / PLoS Genetics)

3. Estimated month of submission: Jan 2012

Tfbs turnover in liver (integrate with ChIP seq) Martin

• Outline: Integration of cross-species ChIP-seq data in liver with proximal CAGE tag cluster responses in the same species. Data on liver ChIP-seq for the transcription factors HNF1A and CEBPA in human/mouse/dog/(chicken) Schmidt et al, Science 2010 has been obtained. The questions we can address with this study are:
  • Are conserved binding sites more likely than non-conserved sites to elicit a local, hepatocyte specific ranscriptional response? (Use CEBPA non-expressing cells to generate a background model of proximal transcriptional responses). This could be used to estimate "functional turnover" as opposed to the "binding turnover" as reported by Duncan Odom.
  • Does hepatocyte specific expression (around binding sites) segregate through species lineages with the experimentally defined binding site?
  • If there is apparent turn-over of binding sites, is the pattern of local responsive transcription conserved?
  • Do we see conservation of hepatocyte specific transcriptional responses even in the absence of binding site conservation?
• Group members: Martin Taylor, Alison Meynert

1. Interested in including in special issue: Y

2. Appropriate journal for this article:(Genome Research / Genome Biology / PLoS Genetics)

3. Estimated month of submission: Dec 2011

Selective vulnerability for neurodegenerative disease (Peter Heutink)

• Outline:One of the most intriguing questions in neuroscience is the functional differentiation of the brain and the selective vulnerability of specific regions to neurodegenerative diseases. Why do mutations in ubiquitously expressed genes result in pathology only in specifically defined regions? Although the phenomenon itself is well documented, its molecular basis is largely unknown. The answer must come from detailed studies on gene and protein expression. Therefore, we will built a genome-wide inventory of noncoding and protein-coding transcripts (transcriptomes) and their promoters (promoteromes) for a series of brain regions in aged human individuals.

We have a series of disease brains available for validation

• Group members: Peter Heutink, Margherita Francescato, Albin Sandelin, Al Forrest and anyone who is interested

1. Interested in including in special issue: Y

2. Appropriate journal for this article:(Genome Research, Neuron)

3. Estimated month of submission: march/2012

Rett syndrome and visual cortex Alka

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Genomic architecture in 3 genes involved in Rett syndrome Alka

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Genomic architecture of neurodegenerative disease (Gustincich talk P.H., etc.)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Pre-initiation complex (PIC) composition, cell-type specific promoter usage and TC characteristics (Albin)

• Outline: From previous studies (including the FANTOM3 main papers) we know that the positional distributions of TSSs (broadness) and sequence characteristics of used promoters vary across tissues and cell types. Moreover, it is known that certain tissues, e.g. testis and ovary, express variant PIC factors that may cause specific promoter usage. In this project, we aim at investigating the PIC diversity across FANTOM5 samples in relation to TC characteristics (sequence composition, broadness, shape, specificity). Here, we will most likely have a brain focus and hopefully in collaboration with Peter Heutink.
• Group members: Robin Andersson, Eivind Valen, Yun Chen, Albin Sandelin

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Others

Olfactory receptors

• Outline: Promoters of Olfactory receptors (ORs) are still poorly documented. We have an unpublished promoter list for mouse, and CAGE libraries from human olfactory mucosa will be made. We will identify the promoters of the human ORs and analyse their structure. Many ORs have alternative promoters and this is a potential example for the promotorome paper. Human-specific OR promoters might be found. There is evidence of expression of the ORs outside the mouse and human olfactory mucosa, and this satellite paper will report this. Experiments to find a ligand and propose a function may be carried out. More information on the page: Olfactory receptors.
• Group members: Charles Plessy, Giovanni Pascarella, Stefano Gustincich and others, but I am too shy to add their name without asking.

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: on hold

Cell-Cell communicatome (Al forrest)

• Outline: We have possibly the broadest expression map to date. The idea behind this paper will look at the expression of cell surface receptors and ligands (secreted and membrane bound) in the primary cell collection to examine which cells can communicate with which other cells. The receptor-ligand pairing will rely on published interactions. This will build a network where primary cell types are the nodes and receptor-ligand interactions are the edges.

• Group members: none assigned yet

1. Interested in including in special issue: Y

2. Appropriate journal for this article: Genome Research, Molecular Systems Biology, Genome Biology

3. Estimated month of submission: month/year

Drugable cells: drug targets (Al Forrest)

• Outline: We have possibly the broadest expression map to date. The idea behind this paper will look at the cell(and tissue) restriction of known drug targets. Given that we generally want to target one cell type (cancer) or organ, what does this expression profile tell us about undesired side effects due to the drug affecting other cells expressing the drug target.

• Group members: none assigned yet

1. Interested in including in special issue: Y

2. Appropriate journal for this article:Genome Research, Genome Biology

3. Estimated month of submission: month/year

Definition of stem or precursors relationship (Claudio Schneider)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Gene regulation in cells of connective tissues (Vlad, Kim)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Transdifferentiation and network rewiring (Haru; WP6 + others) POTENTIAL main paper for later stage

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Regulatory network in cell lineage tree (Carsten wp5)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Determination of conserved CAGE (Vlad)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Promoting human uniqueness: human-specific promoters of regulatory lncRNA genes drive cis- and trans-regulation. (LL)

• some BACKGROUND on our past work and F5 plans here: Media:FANTOM5-LL.ppt
  
• More information, anticipated Abstract, Definitions, Plan of Work at: Regulatory lncRNAs: 'promoting' human uniqueness
  
• Outline: In FANTOM3, we described complex loci -- sense-antisense pairs Media:F5_human_sense-antisense_pairs_hg19.zip, bidirectional promoters, and gene chains -- prevalent in mammalian genomes. These complex loci often contain long non-coding RNA (lncRNA) genes. Please see Media:F5_human_lncRNAome(Jia&Lipovich_Gencode_Lander).xls for our complete reference list of human lncRNA genes, the human lncRNAome; and Media:F5_human_lncRNAome(Jia&Lipovich_Gencode)BED.zip for our BED file of the Gencode and our Jia et al lncRNAs. LncRNA Genes are often not conserved between mouse and human. Now in FANTOM5, our goal is to functionally characterize the specific contribution of non-conserved sequences in human, particularly promoters of lncRNA genes, to gene regulation at complex loci. We will reach this goal by: 
  

1. identifying all "human-specific" (definition = primate-specific; thus absent in the F5 nonhuman species) promoters in CAGE and CAGEscan data.
   
2. using F5 Cluster Annotation results to find all lncRNA genes whose promoters are human-specific.
   
3. determining which lncRNA genes with human-specific promoters are in complex loci, as defined in the first sentence of this Outline.
   
4. testing each complex locus from #4 for the existence of a unique cis-regulatory expression signature (simple e.g.: all genes in the complex locus are on, all off, or some on and specific others off) that corresponds to a specific cell type, tissue type, steady state, OR TIMECOURSE. TWO PRIMATE-SPECIFIC EXAMPLES: LncRNA AK125271 (co-expressed with and cis-antisense to LBX2 homeobox) up in melanocytic induction over time and up in LPS but down in influenza over time, macrophages; lncRNA ASFMR1 (cis-antisense to FMR1, Fragile X Mental Retardation) up only in influenza after 7 hrs, but not in LPS, over time, macrophages; see slide 7. Signatures are defined both by an expression pattern and by an adjacency, overlap, and specific order / orientation of the co-expressed genes neighboring along the genome.
   
5. determining whether, and how, each complex-locus steady-state-specific expression signature is dependent upon the human-specific promoter of the lncRNA within that signature. (Implementation details are at: Regulatory lncRNAs: 'promoting' human uniqueness ) 
   
6. identifying lncRNA genes whose human-specific promoters have evidence of recent functional constraint or recent positive selection.
   
7. performing, for lncRNAs of exceptional interest based on #5 and #6, reverse-genetic experiments in cell culture to validate whether the human-specific promoter of the lncRNA really has a regulatory impact that contributes to defining a particular steady state. (Note: we would need the OSC's direct help with wet-lab validations. Let's discuss.) 
   
8. defining the unique functional proteome space (e.g. gene ontologies? positive selection? brain genes? etc) cis-regulated by human-specific lncRNA promoters.
   
9. finally, deriving a multidimensional unified cis- and trans-regulatory network that describes human-specific and lncRNA-mediated gene regulation in specific cellular states. Nodes (regulatory lncRNAs and transcription factors) will be shared between the cis-regulatory network (regulation based on genomic overlap or adjacency) and the trans-regulatory network (regulation based on TF-target or known lncRNA-TF relationships). (Definition of such a network is at: Regulatory lncRNAs: 'promoting' human uniqueness )
   

• Group members: Leonard Lipovich, Yulia Medvedeva, Vlad Bajic and lab, Mamoom Rashid, Nicolas Bertin (User:Nbertin), (inviting you to join - please confirm: Jess Mar; John Quackenbush & colleagues), and I am also too shy to name (or invite) potential others. Please email me or the F5 list, or please just add yourselves to this page, if you would like to join this effort.

1. Interested in including in special issue: YES

2. Appropriate journal for this article:Nature Genetics, Genome Research, or any PLoS journal (except PLoS ONE)

3. Estimated month of submission: Jan 2012

Using single direction promoter ti eliminate noise (Yulia)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Specific transcript (Human) regulation and what are nover TF in human (Haru)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Identification of TFBS by de novo methods (Vlad; Boris)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Predicted homotypic clusters and motif prediction (Yulia)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Identification fo features of primates specific promoters (?; together with LL)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Regulation specificity of cells and tissues (Vlad’ s group)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Host pathogen infection relationship; influenza virus, Mycobacteria, Salomonella (Arnab)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Searching for viruses, cryptic viruses (Arnab, mamoon, al, nico)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Deorphanizing transcription factors (Vlad)

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Variation in small RNA population and variation in siRNA machinery (Max)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Cellular restriction of terminal ligases in ubiquitin system (Max)

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Papers of individual cells time courses

• Outline: bla
• Group members: xxx, yyy, zzz

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Extend rat gene models with CAGEscan

• Outline: Rat gene models sometimes lack a proper 5′ UTR. CAGEscan data has been produced using the same RNA (10009-101B8) as the reference FANTOM5 Helicos CAGE library CNhs10612. This experimental data can be used to propose an update of the rat gene models.
• Group members: Charles Plessy, Albin Sandelin, Mette Jørgensen, Johannes Waage, other people, please list yourself.

1. Interested in including in special issue: Y

2. Appropriate journal for this article: Genome Biology

3. Estimated month of submission: On hold

Novel metrics for promoter activity profiles

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

A functional lineage map of mammalian cells using Pathway Fingerprinting Win Hide

1. Interested in including in special issue: Y/N Y

2. Appropriate journal for this article:(provide name please) Gene and Development, Genome Research,

3. Estimated month of submission: month/year Jan 2012

Cellular restriction of epigenomic regulation Erik A. + Andreas Lenn.

• Outline: We aim to map cell and differentiation specific expression and usage of alternative transcription start sites of chromatin remodellers, histone chaperones and other chromatin modifying enzymes.
• Group members: Erik Arner, Andreas Lennartsson

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Epithelial-mesenchymal transition (Soichi)

• Outline: We aim to identify transcriptional network regulating epithelial-mesenchymal transition (EMT) as a mechanism of cancer invasion, and to reveal "cancer invasion attractor" along with time-course of EMT. Clarification of transcriptional network and its maintaining "cancer invasion attractor" allows us to develop a translocation inhibitor drug.
• Group members: Soichi Ogishima, Ken Miyguchi, Hideyuki Saya, Hiroshi Tanaka, ... (welcome to join us)

1. Interested in including in special issue: Yes

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Evaluation of CAGE clusters using chromatin marks (Drablos, Rye)

• Using chromatin marks from different cell-lines to evaluate CAGE tag clusters.

Preliminary report: Media:CAGE_cluster_evaluation_Drablos_Rye_13012012.pdf

Table with scored clusters: [1]

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: 2012

Regulatory elements within gene-bodies (Finn Drabløs' group)

Outline: Having integrated ENCODE data from ChIP-Seq of transcription factors and histone modifications in two cell lines (K562 and Gm12878), we have identified regulatory elements within gene-bodies of both transcribed and silent genes. We seek to investigate the classification an biological role of these regulatory elements. One of the questions we will answer is whether downstream elements are different from upstream elements. Integrating CAGE-tags, in addition to HI-C (and ChIA-PET?) will be used to address whether these elements produce transcripts or are involved in long-range interactions, or whether they target mainly the host gene or other genes.

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:Genome Biology

3. Estimated month of submission: 2012

Co-expressed genes associated with ChIP-Seq TF-peak clusters (Finn Drabløs' group)

Outline: We look at experimentally determined ChIP-Seq transcription factor peaks from two (or three) ENCODE cell-lines (K562, Gm12878 and possibly HeLaS3). We identify peak-clusters, and a part of the paper will be to look at correlations of expression profiles of genes regulated by the same TFs, or TF-clusters over all CAGE tissues/cell-types. The main focus will be on ENCODE-data integration, but with CAGE-tags as an important component, for gene expression profiles. Using HI-C data to look for co-expression of genes located close together on the genome (in relation to TF ChIP-Seq peaks) is also interesting.

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:Genome Biology

3. Estimated month of submission: 2012

Analysis of X-linked Promoter Activity between Male and Female Samples (Wyeth Wasserman's group)

• Outline:
• Group members: Wyeth Wasserman, Julie Chih-yu Chen, Anthony Mathelier, Rebecca Worsley Hunt

1. Interested in including in special issue: Y/N

2. Appropriate journal for this article:(provide name please)

3. Estimated month of submission: month/year

Issues: negotiation with sample providers

Encouraged to write paper, but larger stronger papers is perhaps better?

The above is a tentative list of satellite manuscripts listed at the Ume meeting. Please take the time to fill in a brief description/abstract of the manuscript and read what others are proposing. Consider whether working together on a combined manuscript will generate a stronger (higher impact) manuscript.

Talk with collaborator before the datasets is published

As mentioned at the Ume meeting. We are working together as a consortium which shares samples, analyses and ideas. Please talk to the sample providers and analysts if you are using a particular subset of the data. If you are uncertain about whether a dataset has particular strings attached please check the collaborator column on the Helicos data production schedule file on the front page. Samples labelled as "FANTOM5 OSC core" are largely free for use. If you want to use data generated on samples by a particular collaborator please contact them.