# Transcriptomics Explorer **URL:** https://community.brain-map.org/c/transcriptomics-viewer/12.md [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) --- ## [Extracting data from whole cortex+hippocampus transcrip.tome data set](https://community.brain-map.org/t/extracting-data-from-whole-cortex-hippocampus-transcrip-tome-data-set/354)
**Author:** [@Tuomo](https://community.brain-map.org/u/Tuomo)\ **Replies:** 1\ **Last updated:** [November 19, 2019, 10:16pm UTC](https://community.brain-map.org/t/extracting-data-from-whole-cortex-hippocampus-transcrip-tome-data-set/354 "2019-11-19T22:16:03Z")
Thank you for making this great data set available. A couple of diverse questions on data analysis. Are cells from prefrontal cortex included in the data? When I check through the ‘region\_label’ entry of all 76308 cel… --- ## [Metadata of mouse whole cortex and hippocampus 10x data set](https://community.brain-map.org/t/metadata-of-mouse-whole-cortex-and-hippocampus-10x-data-set/732)
**Author:** [@Michael](https://community.brain-map.org/u/Michael)\ **Replies:** 6\ **Last updated:** [September 8, 2021, 8:16pm UTC](https://community.brain-map.org/t/metadata-of-mouse-whole-cortex-and-hippocampus-10x-data-set/732 "2021-09-08T20:16:56Z")
I recently downloaded the “mouse whole cortex and hippocampus 10x” data set. As a first step, I loaded the “gene expression matrix” with python and created a tSNE plot. Individual data points were colored according to th… --- ## [What brain regions are denoted as M1ul/M1lm and S1ul/S1lm?](https://community.brain-map.org/t/what-brain-regions-are-denoted-as-m1ul-m1lm-and-s1ul-s1lm/525)
**Author:** [@amygdala](https://community.brain-map.org/u/amygdala)\ **Replies:** 1\ **Last updated:** [April 27, 2020, 6:26pm UTC](https://community.brain-map.org/t/what-brain-regions-are-denoted-as-m1ul-m1lm-and-s1ul-s1lm/525 "2020-04-27T18:26:02Z")
Hey all, I’m looking through the human transcriptomics explorer and I noticed the above terms. I’m guessing M1/S1 is in regards to the primary motor cortex and primary sensory cortex but I’m struggling to understand the… --- ## [Getting Started: Gene Expression Heatmap](https://community.brain-map.org/t/getting-started-gene-expression-heatmap/663)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [August 12, 2020, 3:55pm UTC](https://community.brain-map.org/t/getting-started-gene-expression-heatmap/663 "2020-08-12T15:55:47Z")
The Heatmap visualization shows a heatmap of gene expression across the taxonomy of Cell Types for the current dataset. The default genes displayed provide waypoints across the taxonomy as a whole. The colors depict the … --- ## [List of Cell-Type and/or Cluster Markers](https://community.brain-map.org/t/list-of-cell-type-and-or-cluster-markers/1068)
**Author:** [@AndyCGraham](https://community.brain-map.org/u/AndyCGraham)\ **Replies:** 4\ **Last updated:** [August 9, 2022, 4:41pm UTC](https://community.brain-map.org/t/list-of-cell-type-and-or-cluster-markers/1068 "2022-08-09T16:41:08Z")
Hi, Is there a way to extract marker genes for each cell-type or cluster, or is it required to download the data and perform differential expression testing offline? Thanks. --- ## [How do I find genes that differentiate Cell Types? (differential search)](https://community.brain-map.org/t/how-do-i-find-genes-that-differentiate-cell-types-differential-search/277)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [September 17, 2019, 12:53am UTC](https://community.brain-map.org/t/how-do-i-find-genes-that-differentiate-cell-types-differential-search/277 "2019-09-17T00:53:25Z")
Differential search is not currently supported in the Transcriptomics Explorer. This functionality is under development and planned for release in 2020. Example use cases or additional requests are welcome on this thread… --- ## [Citation for Allen scRNAseq Mouse and Human datasets](https://community.brain-map.org/t/citation-for-allen-scrnaseq-mouse-and-human-datasets/491)
**Author:** [@vivek.mahadevan](https://community.brain-map.org/u/vivek.mahadevan)\ **Replies:** 4\ **Last updated:** [March 30, 2020, 3:01am UTC](https://community.brain-map.org/t/citation-for-allen-scrnaseq-mouse-and-human-datasets/491 "2020-03-30T03:01:15Z")
Hello, I have downloaded and re-analyzed the pan-GABAergic, pan-glutamatergic scRNAseq dataset derived from mouse hippocampus and cortex, obtained from the Allen portal: https://portal.brain-map.org/atlases-and-data/rn… --- ## [How to set median data in transcriptomics explorer in human datasets?](https://community.brain-map.org/t/how-to-set-median-data-in-transcriptomics-explorer-in-human-datasets/601)
**Author:** [@Christos](https://community.brain-map.org/u/Christos)\ **Replies:** 8\ **Last updated:** [November 3, 2020, 8:57pm UTC](https://community.brain-map.org/t/how-to-set-median-data-in-transcriptomics-explorer-in-human-datasets/601 "2020-11-03T20:57:57Z")
How to set median data in transcriptomics explorer in human datasets? Currently, only trimmed mean data are visible in the heatmap. --- ## [Getting Started with the Transcriptomics Explorer](https://community.brain-map.org/t/getting-started-with-the-transcriptomics-explorer/271)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 2\ **Last updated:** [March 21, 2023, 3:01pm UTC](https://community.brain-map.org/t/getting-started-with-the-transcriptomics-explorer/271 "2023-03-21T15:01:16Z")
Overview The Transcriptomics Explorer is a browser-based tool for researchers to visualize and analyze scRNA sequencing data and related cell types for both mouse and human. A previous version of this tool - called the … --- ## [Getting Started: Dataset Sampling Strategy](https://community.brain-map.org/t/getting-started-dataset-sampling-strategy/665)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [August 12, 2020, 3:57pm UTC](https://community.brain-map.org/t/getting-started-dataset-sampling-strategy/665 "2020-08-12T15:57:15Z")
The Sampling Strategy visualization illustrates the distribution of cells in the dataset across classes, subclasses, and dimensions of the experimental design, such as brain region. The area of each blue dot represents t… --- ## [CPM normalization of 10X mouse single-cell RNA-seq](https://community.brain-map.org/t/cpm-normalization-of-10x-mouse-single-cell-rna-seq/1242)
**Author:** [@RandallJEllis](https://community.brain-map.org/u/RandallJEllis)\ **Replies:** 2\ **Last updated:** [August 25, 2021, 7:25pm UTC](https://community.brain-map.org/t/cpm-normalization-of-10x-mouse-single-cell-rna-seq/1242 "2021-08-25T19:25:51Z")
I am using the “WHOLE CORTEX & HIPPOCAMPUS - 10X GENOMICS (2020) WITH 10X-SMART-SEQ TAXONOMY (2020)” dataset, and I’m wanting to look at how certain genes are expressed in different clusters, regions, and subclasses, and… --- ## [From electrophysiology to t-types](https://community.brain-map.org/t/from-electrophysiology-to-t-types/646)
**Author:** [@Anatoly](https://community.brain-map.org/u/Anatoly)\ **Replies:** 2\ **Last updated:** [August 7, 2020, 6:24pm UTC](https://community.brain-map.org/t/from-electrophysiology-to-t-types/646 "2020-08-07T18:24:54Z")
Hi everybody, I hope everyone is doing well during these challenging times. I would like to ask the community about the t-types. We are currently working in human patch-seq problem on identification the relationship bet… --- ## [How to set median data in transcriptomics explorer in mouse datasets?](https://community.brain-map.org/t/how-to-set-median-data-in-transcriptomics-explorer-in-mouse-datasets/600)
**Author:** [@Christos](https://community.brain-map.org/u/Christos)\ **Replies:** 4\ **Last updated:** [July 12, 2020, 7:18pm UTC](https://community.brain-map.org/t/how-to-set-median-data-in-transcriptomics-explorer-in-mouse-datasets/600 "2020-07-12T19:18:44Z")
How to set median data in transcriptomics explorer in mouse datasets? currently, only trimmed means data are seen in the heatmap --- ## [Is the previous version of the site still available somewhere?](https://community.brain-map.org/t/is-the-previous-version-of-the-site-still-available-somewhere/290)
**Author:** [@matt\_johnson](https://community.brain-map.org/u/matt_johnson)\ **Replies:** 2\ **Last updated:** [January 7, 2020, 3:36pm UTC](https://community.brain-map.org/t/is-the-previous-version-of-the-site-still-available-somewhere/290 "2020-01-07T15:36:58Z")
Is the previous version with additional features like differential expression and marker gene search still available somewhere? --- ## [How to convert scRNA gene names to common gene IDs?](https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723)
**Author:** [@dg520](https://community.brain-map.org/u/dg520)\ **Replies:** 2\ **Last updated:** [October 8, 2020, 4:36pm UTC](https://community.brain-map.org/t/how-to-convert-scrna-gene-names-to-common-gene-ids/723 "2020-10-08T16:36:43Z")
Hi all, I’m using Allen Brain’s Human Cortex scRNA data as a reference set in my analysis. I’m trying to integrate my data with Allen Brain’s. However, I found the gene symbols used in Allen Brain’s data seems not compa… --- ## [Non-anonymized BAM files](https://community.brain-map.org/t/non-anonymized-bam-files/494)
**Author:** [@rgescudero](https://community.brain-map.org/u/rgescudero)\ **Replies:** 1\ **Last updated:** [March 26, 2020, 6:53pm UTC](https://community.brain-map.org/t/non-anonymized-bam-files/494 "2020-03-26T18:53:10Z")
I’m interested in analyzing some aberrant splicing events taking place in Alzheimer’s disease, in collaborating with Dr. Jesus Avila. I would like to get acces to the RNA-seq raw data (either fastq or bam files) containi… --- ## [Comparing expression of a subset of genes in a subset or areas across cell types](https://community.brain-map.org/t/comparing-expression-of-a-subset-of-genes-in-a-subset-or-areas-across-cell-types/3580)
**Author:** [@CelineCammarata](https://community.brain-map.org/u/CelineCammarata)\ **Replies:** 5\ **Last updated:** [September 9, 2024, 4:46pm UTC](https://community.brain-map.org/t/comparing-expression-of-a-subset-of-genes-in-a-subset-or-areas-across-cell-types/3580 "2024-09-09T16:46:55Z")
Hi there, I think I have a very basic question. I am trying to use the Mouse whole cortex and hippocampus 10X dataset to do compare expression of cholinergic receptor genes acorss interneurons classes and excitatory cell… --- ## [PKM Splice Variants](https://community.brain-map.org/t/pkm-splice-variants/799)
**Author:** [@Paugust](https://community.brain-map.org/u/Paugust)\ **Replies:** 1\ **Last updated:** [November 26, 2020, 4:56am UTC](https://community.brain-map.org/t/pkm-splice-variants/799 "2020-11-26T04:56:11Z")
I am looking for the differential expression of the two isoforms of PKM1 and PKM2. They do not seem to be represented in the data set by RNASEQ or IHC. Will they be included in future versions? --- ## [Human dopaminergic neurons](https://community.brain-map.org/t/human-dopaminergic-neurons/762)
**Author:** [@sofiapuvogelvittini](https://community.brain-map.org/u/sofiapuvogelvittini)\ **Replies:** 2\ **Last updated:** [November 12, 2020, 9:24am UTC](https://community.brain-map.org/t/human-dopaminergic-neurons/762 "2020-11-12T09:24:16Z")
Hello, I am generating data with human midbrain single nucleus transcriptomic (selecting Neun positive nucleus). I’m trying to identify neuronal subpopulations and so far what seemed best to me was to use your data of … --- ## [Transcriptomic explorere missing information?](https://community.brain-map.org/t/transcriptomic-explorere-missing-information/734)
**Author:** [@Clara](https://community.brain-map.org/u/Clara)\ **Replies:** 1\ **Last updated:** [October 21, 2020, 7:32pm UTC](https://community.brain-map.org/t/transcriptomic-explorere-missing-information/734 "2020-10-21T19:32:46Z")
Hi, I have been using the Transcriptomic Explorer for Mouse brain (both 10X and SMART-seq) before the summer and recently I noticed some changes in the data visualisation in the heatmap. I noticed that many genes I sear… --- ## [Can we download a Heat Map or t-SNE visualisation?](https://community.brain-map.org/t/can-we-download-a-heat-map-or-t-sne-visualisation/542)
**Author:** [@zchor](https://community.brain-map.org/u/zchor)\ **Replies:** 1\ **Last updated:** [May 8, 2020, 10:19pm UTC](https://community.brain-map.org/t/can-we-download-a-heat-map-or-t-sne-visualisation/542 "2020-05-08T22:19:07Z")
I like the visualisation I can produce for my genes of interest, and would like to export that for presentation purposes, referencing the tool of course. Is this possible? And how could I go about doing this? --- ## [Reconstructing the dendrogram shown in the transcriptomics explorer with R based on the .json file](https://community.brain-map.org/t/reconstructing-the-dendrogram-shown-in-the-transcriptomics-explorer-with-r-based-on-the-json-file/743)
**Author:** [@Michael](https://community.brain-map.org/u/Michael)\ **Replies:** 1\ **Last updated:** [October 27, 2020, 12:26am UTC](https://community.brain-map.org/t/reconstructing-the-dendrogram-shown-in-the-transcriptomics-explorer-with-r-based-on-the-json-file/743 "2020-10-27T00:26:05Z")
Is there a way to easily reconstruct the dendrogram shown in the transcriptomics explorer of the “Whole Cortex and Hippocampus 10x” data set with R based on the information stored in the “Taxonomy of clusters” .json file… --- ## [Getting Started: Scatterplot (tSNE or UMAP)](https://community.brain-map.org/t/getting-started-scatterplot-tsne-or-umap/664)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [August 12, 2020, 3:56pm UTC](https://community.brain-map.org/t/getting-started-scatterplot-tsne-or-umap/664 "2020-08-12T15:56:47Z")
The Scatterplot visualization shows each cell in the dataset in a 2D plot, generated from either the tSNE or UMAP algorithms. By default, the dots (cells) are colored by their cell type assignment. At a glance, most cell… --- ## [Is there a way to associate median-cluster cell type aliases with their structure ids?](https://community.brain-map.org/t/is-there-a-way-to-associate-median-cluster-cell-type-aliases-with-their-structure-ids/1064)
**Author:** [@cornhundred](https://community.brain-map.org/u/cornhundred)\ **Replies:** 2\ **Last updated:** [May 4, 2021, 7:30pm UTC](https://community.brain-map.org/t/is-there-a-way-to-associate-median-cluster-cell-type-aliases-with-their-structure-ids/1064 "2021-05-04T19:30:09Z")
Hi, is there a way to associate mouse cell type aliases from the median clusters (e.g. columns from the transcriptomics explorer) with their associated Structure IDs? I would like to know where these cell types are prese… --- ## [Subsetting Mouse Whole Cortex and Hippocampus 10x data by brain region?](https://community.brain-map.org/t/subsetting-mouse-whole-cortex-and-hippocampus-10x-data-by-brain-region/2439)
**Author:** [@kesavell](https://community.brain-map.org/u/kesavell)\ **Replies:** 1\ **Last updated:** [July 7, 2023, 7:50pm UTC](https://community.brain-map.org/t/subsetting-mouse-whole-cortex-and-hippocampus-10x-data-by-brain-region/2439 "2023-07-07T19:50:44Z")
We want to compare our snRNAseq data cell types to the Mouse Whole Cortex and Hippocampus 10x dataset. We want to do this for the corresponding brain region only. Has anyone successfully subset the large 10X gene expres… --- ## [How do I find marker genes for a Cell Type or Cell Set?](https://community.brain-map.org/t/how-do-i-find-marker-genes-for-a-cell-type-or-cell-set/276)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [September 17, 2019, 12:52am UTC](https://community.brain-map.org/t/how-do-i-find-marker-genes-for-a-cell-type-or-cell-set/276 "2019-09-17T00:52:22Z")
Currently the Transcriptomics Explorer loads with a set of notable genes that characterize the entire taxonomy. The Explorer does not currently expose marker genes for every Cell Type or Cell Set - that functionality is … --- ## [Is there a way to subset ORB from PL;ILA;ORB?](https://community.brain-map.org/t/is-there-a-way-to-subset-orb-from-pl-ila-orb/1749)
**Author:** [@RandallJEllis](https://community.brain-map.org/u/RandallJEllis)\ **Replies:** 1\ **Last updated:** [August 11, 2022, 5:32pm UTC](https://community.brain-map.org/t/is-there-a-way-to-subset-orb-from-pl-ila-orb/1749 "2022-08-11T17:32:48Z")
In the scRNA-seq data, there’s a region\_label for PL;ILA;ORB. I am wondering if there’s any possible way to subset just the ORB cells. --- ## [Does Allen brain provide user open source to build transcriptomics explorer?](https://community.brain-map.org/t/does-allen-brain-provide-user-open-source-to-build-transcriptomics-explorer/636)
**Author:** [@namuk](https://community.brain-map.org/u/namuk)\ **Replies:** 1\ **Last updated:** [July 24, 2020, 6:03pm UTC](https://community.brain-map.org/t/does-allen-brain-provide-user-open-source-to-build-transcriptomics-explorer/636 "2020-07-24T18:03:29Z")
Hello. My name is Nam-uk Kim from the Korea Brain Research Institute. I have a some questions. I am trying to build a web based explorer like the site transcriptomics explorer below. : https://celltypes.brain-map.org… --- ## [Can I map my own data to these data sets?](https://community.brain-map.org/t/can-i-map-my-own-data-to-these-data-sets/279)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [September 17, 2019, 6:48pm UTC](https://community.brain-map.org/t/can-i-map-my-own-data-to-these-data-sets/279 "2019-09-17T18:48:03Z")
Currently it is not possible for researchers to directly map their data to taxonomies available in the Transcriptomics Explorer. Researchers interested in mapping their data can reply to this post for support from an All… --- ## [What datasets are available in the Transcriptomics Viewer?](https://community.brain-map.org/t/what-datasets-are-available-in-the-transcriptomics-viewer/255)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [September 3, 2019, 6:34pm UTC](https://community.brain-map.org/t/what-datasets-are-available-in-the-transcriptomics-viewer/255 "2019-09-03T18:34:59Z")
Currently two datasets are available: Mouse: 75,000 cells from across the cortex and hippocampus, analyzed with SMART-seq. Learn more about this dataset or review the protocols used to generate and analyze the data. Hu… --- ## [New Genome Browser views for single cell/nucleus transcriptomics!](https://community.brain-map.org/t/new-genome-browser-views-for-single-cell-nucleus-transcriptomics/889)
**Author:** [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\ **Replies:** 0\ **Last updated:** [January 13, 2021, 4:51am UTC](https://community.brain-map.org/t/new-genome-browser-views-for-single-cell-nucleus-transcriptomics/889 "2021-01-13T04:51:34Z")
Base pair-level visualization of several single cell/nucleus RNA-seq taxonomies are now available through the UCSC Genome Browser. To access this new tool, go to the Allen Cell Types Database: RNA-seq data, click on the… --- ## [Supported browsers](https://community.brain-map.org/t/supported-browsers/438)
**Author:** [@tylermo](https://community.brain-map.org/u/tylermo)\ **Replies:** 0\ **Last updated:** [February 7, 2020, 1:36am UTC](https://community.brain-map.org/t/supported-browsers/438 "2020-02-07T01:36:19Z")
Optimal browsers are the latest version of: Chrome Firefox Safari Edge Unfortunately, as of Jan 2020, IE11 and Microsoft Edge do not support key functionality for the Transcriptomics Explorer, so experience through th… --- ## [Human Forebrain Genome Data](https://community.brain-map.org/t/human-forebrain-genome-data/2231)
**Author:** [@brainr3search](https://community.brain-map.org/u/brainr3search)\ **Replies:** 1\ **Last updated:** [March 14, 2023, 4:33am UTC](https://community.brain-map.org/t/human-forebrain-genome-data/2231 "2023-03-14T04:33:14Z")
Greetings, I am new to the platform, and do not know how to use the brain explorer to download or search data. Currently, I am looking for Human Forebrain Genome Data. Would someone mind assisting or giving feedback on … --- ## [Known protein not detected by RNA explorer](https://community.brain-map.org/t/known-protein-not-detected-by-rna-explorer/3109)
**Author:** [@jackp](https://community.brain-map.org/u/jackp)\ **Replies:** 1\ **Last updated:** [February 29, 2024, 7:31pm UTC](https://community.brain-map.org/t/known-protein-not-detected-by-rna-explorer/3109 "2024-02-29T19:31:50Z")
I recently used the RNA explorer (10x and SMART-seq) to view expression of the mechanosensitive channel Piezo1 which is known to be expressed in the motor cortex and hippocampus of mice. The heatmap results did not show … --- ## [RNA expression values on heat map Developmental Transcriptome do not match database](https://community.brain-map.org/t/rna-expression-values-on-heat-map-developmental-transcriptome-do-not-match-database/4727)
**Author:** [@mshtrahman](https://community.brain-map.org/u/mshtrahman)\ **Replies:** 3\ **Last updated:** [October 31, 2025, 3:16pm UTC](https://community.brain-map.org/t/rna-expression-values-on-heat-map-developmental-transcriptome-do-not-match-database/4727 "2025-10-31T15:16:37Z")
When browsing the Developmental Transcriptome “Gene Level RPKM” viewer, I noticed that the expression values (in log RPKM) in the heat map do not match the values for the same gene (same entrez number and name) in the “e… --- ## [Cell Types Database: RNA-Seq Data](https://community.brain-map.org/t/cell-types-database-rna-seq-data/4246)
**Author:** [@RebecaO](https://community.brain-map.org/u/RebecaO)\ **Replies:** 1\ **Last updated:** [March 14, 2025, 8:55pm UTC](https://community.brain-map.org/t/cell-types-database-rna-seq-data/4246 "2025-03-14T20:55:17Z")
Hi! I want to compare some cortical snRNA-seq data with a reference dataset. I’ve seen this reference dataset \[ Whole Cortex & Hippocampus - SMART-seq (2019) with 10x-SMART-seq taxonomy (2021)\] but it is too big to work… --- ## [Connectivity.brain-map.org still down / blank page as of November 2025](https://community.brain-map.org/t/connectivity-brain-map-org-still-down-blank-page-as-of-november-2025/4762)
**Author:** [@chordata123](https://community.brain-map.org/u/chordata123)\ **Replies:** 2\ **Last updated:** [November 15, 2025, 12:24am UTC](https://community.brain-map.org/t/connectivity-brain-map-org-still-down-blank-page-as-of-november-2025/4762 "2025-11-15T00:24:53Z")
The Mouse Connectivity Atlas at https://connectivity.brain-map.org/ is currently not loading properly. It only shows a blank page with a dash line (no interface, no errors, just empty). - This has been ongoing for at le… --- ## [Deconvolution of mice bulk hippocampal transcriptomics](https://community.brain-map.org/t/deconvolution-of-mice-bulk-hippocampal-transcriptomics/4812)
**Author:** [@lciaran](https://community.brain-map.org/u/lciaran)\ **Replies:** 1\ **Last updated:** [January 12, 2026, 6:31pm UTC](https://community.brain-map.org/t/deconvolution-of-mice-bulk-hippocampal-transcriptomics/4812 "2026-01-12T18:31:30Z")
Hi! I have performed bulk hippocampal transcriptomics in mice and I’m interested in performing deconvolution to separate the different cell types. Is there a suitable database which I can use as my matrix and which metho… --- ## [Ensembl ID and gene name not matching](https://community.brain-map.org/t/ensembl-id-and-gene-name-not-matching/4706)
**Author:** [@maddym](https://community.brain-map.org/u/maddym)\ **Replies:** 1\ **Last updated:** [September 26, 2025, 6:45pm UTC](https://community.brain-map.org/t/ensembl-id-and-gene-name-not-matching/4706 "2025-09-26T18:45:42Z")
Hello there, I am trying to process some specific gene data and it looks like there are some discrepancies in Ensembl IDs and gene names between the Allen Atlas and other sources. I am curious if there is a way to troubl… --- ## [Gene Thresholds](https://community.brain-map.org/t/gene-thresholds/4864)
**Author:** [@vfiello](https://community.brain-map.org/u/vfiello)\ **Replies:** 1\ **Last updated:** [March 27, 2026, 3:35pm UTC](https://community.brain-map.org/t/gene-thresholds/4864 "2026-03-27T15:35:10Z")
Hello! I’m relatively new here and trying to use NEMO to explore the datasets, but it’s asking for a gene threshold. Is the only way to access specific gene thresholds is through Jupyter and Python? Are there any ways o… --- ## [Seeking Single-Cell Expression Data in Intergenic Regions](https://community.brain-map.org/t/seeking-single-cell-expression-data-in-intergenic-regions/4071)
**Author:** [@Elliot](https://community.brain-map.org/u/Elliot)\ **Replies:** 1\ **Last updated:** [January 17, 2025, 3:39pm UTC](https://community.brain-map.org/t/seeking-single-cell-expression-data-in-intergenic-regions/4071 "2025-01-17T15:39:44Z")
Good morning, I am looking for single-cell expression data specifically in intergenic regions. However, I have been unable to find expression data for non-coding regions. Does such data exist? If not, are there .bigwig …