Brain expression

This page contains information used for various brain transcriptome projects.

Downloaded datasets

Are under /cortex/data. For example

Mouse development microarray data is under /cortex/data/microarray/mouse/dev_compendium/

The main datasets we use:

• • Kang2011: Human, 16 regions, 57 subjects, 490 samples, microarray. [/cortex/data/microarray/human/Kang2011]

• 6Humans: Human, many regions, 6 subjects, ~3700 samples, microarray.

• Zapalla2005: Mouse, 19 regions, 80 samples, microarray

• [/cortex/data/microarray/mouse/Zapalla2005]

• Su2004: Mouse brain regions

• AllenMouseDev: Mouse, 7 ages, 11 regions, ISH

  • brainspan2014: Human, 16 regions, 57 subjects, X samples, RNAseq.

  • [/cortex/data/RNAseq/human/brainspan2014]

Download new datasets from NCBI-GEO

Here is an example

mkdir /cortex/data/microarray/human/Giger2010

maltab

>> addpath('/cortex/code/matlab/download_GEO_data/')

>> OUTPUT_DIR='/cortex/data/microarray/human/Giger2010'

>> get_GSE_data('GSE12293', OUTPUT_DIR)

In case the data contains multiple GPLs the following error will show

Error using getgeodata_local_overwrite (line 180)

The GSE record contains multiple files. These were copied to /tmp/tpba95349d_b0f9_4cfc_8f24_05ec01459cf2. Please use GEOSERIESREAD

to read the data from this directory.

Error in get_GSE_data (line 53)

In that case, ls gives

>> ls /tmp/tpba95349d_b0f9_4cfc_8f24_05ec01459cf2

GSE12293-GPL570_series_matrix.txt

GSE12293-GPL81_series_matrix.txt

So now rerun get_GSE_data with the GPL you are interested in:

filename = '/tmp/tpba95349d_b0f9_4cfc_8f24_05ec01459cf2/GSE12293-GPL81_series_matrix.txt'

get_GSE_data(filename, OUTPUT_DIR)

Brain-related KEGG pathways (brite hierarchy)

• 1. hsa04713 Circadian entrainment

Nervous system

• 1. hsa04720 Long-term potentiation

  2. hsa04721 Synaptic vesicle cycle

  3. hsa04722 Neurotrophin signaling pathway

  4. hsa04723 Retrograde endocannabinoid signaling

  5. hsa04724 Glutamatergic synapse

  6. hsa04725 Cholinergic synapse

  7. hsa04726 Serotonin

  8. hsa04727 GABAergic synapse

  9. hsa04728 dopamine

  10. hsa04730 Long-term depression

Sensory system

• 1. hsa04740 Olfactory transduction

  2. hsa04742 Taste transduction

  3. hsa04744 Phoro transduction

Neurodegenerative diseases

• 1. hsa05012 Parkinson's disease

  2. hsa05012 Alzheimer's disease

  3. hsa05014 Amyotrophic lateral sclerosis (ALS)

  4. hsa05016 Huntington disease

  5. hsa05016 Prion diseases

Substance diseases

• 1. hsa05030 Cocaine addiction

  2. hsa05031 Amphetamine addiction

  3. hsa05032 Morphine addiction

  4. hsa05033 Nicotine addiction

  5. hsa05034 Alcoholism