# \#portal **URL:** https://forum.depmap.org/tag/portal/1.md [Latest](https://forum.depmap.org/latest.md) · [Categories](https://forum.depmap.org/categories.md) · [Tags](https://forum.depmap.org/tags.md) --- ## [TSS\_RRBS\_Methylation\_Data](https://forum.depmap.org/t/tss-rrbs-methylation-data/4659)
**Author:** [@Michele\_Spanu](https://forum.depmap.org/u/Michele_Spanu)\ **Replies:** 0\ **Last updated:** [July 27, 2026, 2:06pm UTC](https://forum.depmap.org/t/tss-rrbs-methylation-data/4659 "2026-07-27T14:06:40Z")
I have noticed that some genes are not available in any of the methylation datasets (CCLE\_RRBS\_TSS\_1kb\_20180614.txt, CCLE\_RRBS\_TSS\_CpG\_clusters\_20180614.txt), but seem to be available through the portal’s Data Explorer. … --- ## [Error when downloading files using custom download](https://forum.depmap.org/t/error-when-downloading-files-using-custom-download/4648)
**Author:** [@Ankita\_Srivastava](https://forum.depmap.org/u/Ankita_Srivastava)\ **Replies:** 2\ **Last updated:** [June 29, 2026, 2:10pm UTC](https://forum.depmap.org/t/error-when-downloading-files-using-custom-download/4648 "2026-06-29T14:10:25Z")
Hi, I am getting the following error when trying to download drug sensitivity and crispr data using custom download for particular model. Please help me resolving this issue. --- ## [Celligner median distances](https://forum.depmap.org/t/celligner-median-distances/4618)
**Author:** [@Laura2](https://forum.depmap.org/u/Laura2)\ **Replies:** 0\ **Last updated:** [April 30, 2026, 3:49pm UTC](https://forum.depmap.org/t/celligner-median-distances/4618 "2026-04-30T15:49:12Z")
Hello! I was wondering how the median distance value is calculated in the Celligner “Rank models for selected tumors” page. For example, if I select “Breast” lineage and “All” subtype, is the median distance displayed … --- ## [Missing CCLE 2019 mutation data download?](https://forum.depmap.org/t/missing-ccle-2019-mutation-data-download/4387)
**Author:** [@cdputnam](https://forum.depmap.org/u/cdputnam)\ **Replies:** 4\ **Last updated:** [April 29, 2026, 1:01pm UTC](https://forum.depmap.org/t/missing-ccle-2019-mutation-data-download/4387 "2026-04-29T13:01:37Z")
In the DepMap Data Portal, the file described as “merged mutation calls” actually points to CCLE\_GlobalChromatinProfiling\_20181130.csv, which as the filename suggests provides global chromatin profiling information and n… --- ## [DepMap portal cell line mutation,](https://forum.depmap.org/t/depmap-portal-cell-line-mutation/4186)
**Author:** [@dizysky](https://forum.depmap.org/u/dizysky)\ **Replies:** 2\ **Last updated:** [May 5, 2025, 3:00pm UTC](https://forum.depmap.org/t/depmap-portal-cell-line-mutation/4186 "2025-05-05T15:00:33Z")
Hello, What version does the DepMap portal use currently to annotate a mutation in a cancer cell line with the default setting? A couple of cell lines showed a different mutation pattern between cBio (broad 2019 data, … --- ## [Copy\_Number\_(Absolute) and OmicsAbsoluteCNGene are Different](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677)
**Author:** [@Mr\_Epimetheus](https://forum.depmap.org/u/Mr_Epimetheus)\ **Replies:** 1\ **Last updated:** [October 24, 2024, 6:09pm UTC](https://forum.depmap.org/t/copy-number-absolute-and-omicsabsolutecngene-are-different/3677 "2024-10-24T18:09:02Z")
Hello, I have noticed that there is a significant difference between the Copy\_Number\_(Absolute) data in the Custom Downloads interface and the OmicsAbsoluteCNGene data in the All Data interface, both in terms of the numb… --- ## [Cell lines removed from newer releases](https://forum.depmap.org/t/cell-lines-removed-from-newer-releases/3627)
**Author:** [@danibrotto](https://forum.depmap.org/u/danibrotto)\ **Replies:** 4\ **Last updated:** [October 7, 2024, 2:13pm UTC](https://forum.depmap.org/t/cell-lines-removed-from-newer-releases/3627 "2024-10-07T14:13:38Z")
Hi! I’m looking to visualize and download CRISPR dependency data from older DepMap releases. I remember that previous versions included more than one chordoma tumor cell line, but they seem to be unavailable in the most … --- ## [Unable to display cell lines from a custom list in graphs](https://forum.depmap.org/t/unable-to-display-cell-lines-from-a-custom-list-in-graphs/3170)
**Author:** [@Andrew\_Cherniack](https://forum.depmap.org/u/Andrew_Cherniack)\ **Replies:** 1\ **Last updated:** [April 5, 2024, 12:25pm UTC](https://forum.depmap.org/t/unable-to-display-cell-lines-from-a-custom-list-in-graphs/3170 "2024-04-05T12:25:42Z")
I uploaded a custom list to the graphing page in the explore your data section, but there doesn’t seem to be anything I can do with these cell lines after that. There are no options to display or color these cell lines … --- ## [Definition of common essential genes](https://forum.depmap.org/t/definition-of-common-essential-genes/3171)
**Author:** [@Allan\_Lui](https://forum.depmap.org/u/Allan_Lui)\ **Replies:** 0\ **Last updated:** [April 2, 2024, 1:00am UTC](https://forum.depmap.org/t/definition-of-common-essential-genes/3171 "2024-04-02T01:00:51Z")
In the web portal, common essential genes are defined as: A gene which, in a large, pan-cancer screen, ranks in the top X most depleting genes in at least 90% of cell lines. X is chosen empirically using the minimum of t… --- ## [Repeated uniprot accesions and weird qvalues of proteomic data in the analysis tool](https://forum.depmap.org/t/repeated-uniprot-accesions-and-weird-qvalues-of-proteomic-data-in-the-analysis-tool/3137)
**Author:** [@lorcai](https://forum.depmap.org/u/lorcai)\ **Replies:** 1\ **Last updated:** [March 20, 2024, 5:11pm UTC](https://forum.depmap.org/t/repeated-uniprot-accesions-and-weird-qvalues-of-proteomic-data-in-the-analysis-tool/3137 "2024-03-20T17:11:06Z")
HI, I have some doubts about how the proteomic data is processed and how the qvalues are calculated on the custom analysis tool. Regarding the data, there are some gene symbols associated to multiple uniprot accesion n… --- ## [Got forbidden 403](https://forum.depmap.org/t/got-forbidden-403/3025)
**Author:** [@Martin\_Akerman](https://forum.depmap.org/u/Martin_Akerman)\ **Replies:** 2\ **Last updated:** [March 7, 2024, 2:11pm UTC](https://forum.depmap.org/t/got-forbidden-403/3025 "2024-03-07T14:11:59Z")
Hello, I was checking manually a list of 48 genes, when I got to 42 I saw the forbidden 403 message and got blocked. I was not running code on the website, just checking if genes were strongly dependent or not, so I was … --- ## [About Depmap page footer](https://forum.depmap.org/t/about-depmap-page-footer/3069)
**Author:** [@temp](https://forum.depmap.org/u/temp)\ **Replies:** 0\ **Last updated:** [February 2, 2024, 2:12pm UTC](https://forum.depmap.org/t/about-depmap-page-footer/3069 "2024-02-02T14:12:50Z")
Hi Phil! :wave: Just a heads up that the footer at the bottom of depmap-homepage seems weirdly sized (and the page might want a header title). (Love the home page!) Cheers, J --- ## [perturbation error](https://forum.depmap.org/t/perturbation-error/3010)
**Author:** [@laimz](https://forum.depmap.org/u/laimz)\ **Replies:** 1\ **Last updated:** [January 17, 2024, 5:30pm UTC](https://forum.depmap.org/t/perturbation-error/3010 "2024-01-17T17:30:19Z")
When I click pertubation, there is an an internal error occurred and I can not continue search. --- ## [Home Page Compound Link Broken](https://forum.depmap.org/t/home-page-compound-link-broken/2947)
**Author:** [@Dario](https://forum.depmap.org/u/Dario)\ **Replies:** 3\ **Last updated:** [December 5, 2023, 9:54pm UTC](https://forum.depmap.org/t/home-page-compound-link-broken/2947 "2023-12-05T21:54:38Z")
On the portal’s home page is Dabrafenib compound overview which leads to 404 Not Found. --- ## [Saved PNG is without data points](https://forum.depmap.org/t/saved-png-is-without-data-points/2937)
**Author:** [@Lorenz\_Eing](https://forum.depmap.org/u/Lorenz_Eing)\ **Replies:** 1\ **Last updated:** [November 28, 2023, 8:38pm UTC](https://forum.depmap.org/t/saved-png-is-without-data-points/2937 "2023-11-28T20:38:53Z")
Hi there, I was just trying to save the 2D Landscape and Biomarker plots (DepMap - Broad Institute). The downloaded png file does not show any data points. It would be great getting according plots somehow and if this … --- ## [Where is probability of dependency used?](https://forum.depmap.org/t/where-is-probability-of-dependency-used/49)
**Author:** [@Jose](https://forum.depmap.org/u/Jose)\ **Replies:** 3\ **Last updated:** [October 24, 2023, 4:23pm UTC](https://forum.depmap.org/t/where-is-probability-of-dependency-used/49 "2023-10-24T16:23:18Z")
When looking at the overview page of a gene it mentions that a cell line is considered dependent if it has a probability of dependency of greater than 0.5., but when I click view details there is no mention of a dependen… --- ## [CCNE1 amplification ](https://forum.depmap.org/t/ccne1-amplification/2840)
**Author:** [@Blast](https://forum.depmap.org/u/Blast)\ **Replies:** 0\ **Last updated:** [September 28, 2023, 8:44pm UTC](https://forum.depmap.org/t/ccne1-amplification/2840 "2023-09-28T20:44:36Z")
CCNE1 amplification is associated with increased sensitivity to PKMYT1 in the literature. Several references talk about confirming this relationship using DepMap (CCNE1 amplification is synthetic lethal with PKMYT1 kina… --- ## [Type of growth media of cell lines](https://forum.depmap.org/t/type-of-growth-media-of-cell-lines/2747)
**Author:** [@Reza](https://forum.depmap.org/u/Reza)\ **Replies:** 3\ **Last updated:** [August 31, 2023, 10:57am UTC](https://forum.depmap.org/t/type-of-growth-media-of-cell-lines/2747 "2023-08-31T10:57:39Z")
Hi there, I found my data for mRNA expression of ELOVL5 in breast cancer cell lines (MCF7, ZR-75-1, T47D). I was wondering if there is any information on the condition of cell line growth including the types of media, a… --- ## [where can i find germline mutation which is defined important?](https://forum.depmap.org/t/where-can-i-find-germline-mutation-which-is-defined-important/2719)
**Author:** [@ohlim](https://forum.depmap.org/u/ohlim)\ **Replies:** 1\ **Last updated:** [July 31, 2023, 5:56pm UTC](https://forum.depmap.org/t/where-can-i-find-germline-mutation-which-is-defined-important/2719 "2023-07-31T17:56:08Z")
hello. first I am new to using depmap. In depmap portal File Downloads there is only somaticmutation files such as OmicsSomaticMutations.maf, csv etc. In the 22Q4 Mutation Pipeline Update i found some germline mutation… --- ## [Missing orange (damaging) and red (hot-spot) dots on perturbation plots](https://forum.depmap.org/t/missing-orange-damaging-and-red-hot-spot-dots-on-perturbation-plots/2637)
**Author:** [@Daniel\_Suveges](https://forum.depmap.org/u/Daniel_Suveges)\ **Replies:** 3\ **Last updated:** [July 12, 2023, 8:53am UTC](https://forum.depmap.org/t/missing-orange-damaging-and-red-hot-spot-dots-on-perturbation-plots/2637 "2023-07-12T08:53:31Z")
Hi Guys, Thank you for developing and maintaining this amazing resource! I have a question, which might as well being a bug: I have noticed that on perturbation view on the gene pages, I can’t see cell lines with damagi… --- ## [Exon-Exon junction counts](https://forum.depmap.org/t/exon-exon-junction-counts/2685)
**Author:** [@MiqG](https://forum.depmap.org/u/MiqG)\ **Replies:** 2\ **Last updated:** [July 11, 2023, 12:59pm UTC](https://forum.depmap.org/t/exon-exon-junction-counts/2685 "2023-07-11T12:59:42Z")
Hi, I have seen in the CCLE 2019 article (Next-generation characterization of the Cancer Cell Line Encyclopedia | Nature) exon-exon junction counts were quantified with STAR to obtain the exon inclusion ratios that are … --- ## [Unable to search anything in the search box](https://forum.depmap.org/t/unable-to-search-anything-in-the-search-box/203)
**Author:** [@jlwu1991](https://forum.depmap.org/u/jlwu1991)\ **Replies:** 7\ **Last updated:** [February 21, 2023, 11:03pm UTC](https://forum.depmap.org/t/unable-to-search-anything-in-the-search-box/203 "2023-02-21T23:03:50Z")
A user report Generally when a gene/compound name typed, the corresponding gene/compound will be listed in the search box. However, recently I was unable to search anything in the search box, anyone could help me out? … --- ## [Predictability tab issue](https://forum.depmap.org/t/predictability-tab-issue/2184)
**Author:** [@Ramono](https://forum.depmap.org/u/Ramono)\ **Replies:** 5\ **Last updated:** [February 8, 2023, 1:27pm UTC](https://forum.depmap.org/t/predictability-tab-issue/2184 "2023-02-08T13:27:26Z")
Hello, Information does not always appear on the predictability page (in particular when searching for the following genes: ZNF471, VIM, WDR4). R. --- ## [keep URLs in download portal](https://forum.depmap.org/t/keep-urls-in-download-portal/2202)
**Author:** [@stbio](https://forum.depmap.org/u/stbio)\ **Replies:** 2\ **Last updated:** [January 12, 2023, 4:59pm UTC](https://forum.depmap.org/t/keep-urls-in-download-portal/2202 "2023-01-12T16:59:27Z")
Hi there! I have a few scripts designed to download DepMap releases from the Portal automatically on a schedule. They’ve been working fine, but recent changes to the download page make that considerably more difficult be… --- ## [Discrepancies in mutational status from Cell line Selector and DepMap mutations tab for cancer cell lines](https://forum.depmap.org/t/discrepancies-in-mutational-status-from-cell-line-selector-and-depmap-mutations-tab-for-cancer-cell-lines/1416)
**Author:** [@Mbgventer](https://forum.depmap.org/u/Mbgventer)\ **Replies:** 6\ **Last updated:** [June 24, 2022, 11:35am UTC](https://forum.depmap.org/t/discrepancies-in-mutational-status-from-cell-line-selector-and-depmap-mutations-tab-for-cancer-cell-lines/1416 "2022-06-24T11:35:04Z")
Dear Community, I hope my message reaches everyone healthy and safe !! I was not sure if I should post my question/issue here, but probably due to the discrepancy of my initial stratification results, I decided to post … --- ## [CRISPR KO the gene of interests](https://forum.depmap.org/t/crispr-ko-the-gene-of-interests/1431)
**Author:** [@MARYAM](https://forum.depmap.org/u/MARYAM)\ **Replies:** 1\ **Last updated:** [June 7, 2022, 7:09pm UTC](https://forum.depmap.org/t/crispr-ko-the-gene-of-interests/1431 "2022-06-07T19:09:06Z")
if the gene of my interest is knockout in cell lines in CRISPR and on the gene effect (Chronos)was zero or positive 0.1 or 0.2 in this case is the cell survive or die? please need an answer. --- ## [Request for a single URL that downloads the latest DepMap Public Release](https://forum.depmap.org/t/request-for-a-single-url-that-downloads-the-latest-depmap-public-release/483)
**Author:** [@dustin.lehmkuhl](https://forum.depmap.org/u/dustin.lehmkuhl)\ **Replies:** 5\ **Last updated:** [May 31, 2022, 5:16am UTC](https://forum.depmap.org/t/request-for-a-single-url-that-downloads-the-latest-depmap-public-release/483 "2022-05-31T05:16:57Z")
Hello, We’ve been using a few of the data releases as they’ve become available and we have started making our own analysis tools in combination with our internally produced data. Are there any plans for making the quart… --- ## [Finding data licenses](https://forum.depmap.org/t/finding-data-licenses/1243)
**Author:** [@dzerbino](https://forum.depmap.org/u/dzerbino)\ **Replies:** 2\ **Last updated:** [March 29, 2022, 4:42pm UTC](https://forum.depmap.org/t/finding-data-licenses/1243 "2022-03-29T16:42:16Z")
Hello, What is the best way to determine the data license governing the usage of a file available for download on the DepMap portal? Thank you, Daniel --- ## [Proteomics data for hnRNPD](https://forum.depmap.org/t/proteomics-data-for-hnrnpd/1249)
**Author:** [@MARYAM](https://forum.depmap.org/u/MARYAM)\ **Replies:** 1\ **Last updated:** [March 18, 2022, 7:57pm UTC](https://forum.depmap.org/t/proteomics-data-for-hnrnpd/1249 "2022-03-18T19:57:52Z")
Hi, I download the data for hnRNPD ( Expression 22Q1 Public) to see the expression of mRNA for cell lines and I saw on the left side of the portal the( proteomics data) and I don’t know what does it mean if any one know … --- ## [How is the # of Dependent Cell Lines a gene is essential for calculated?](https://forum.depmap.org/t/how-is-the-of-dependent-cell-lines-a-gene-is-essential-for-calculated/519)
**Author:** [@Patrick](https://forum.depmap.org/u/Patrick)\ **Replies:** 3\ **Last updated:** [February 4, 2022, 8:30pm UTC](https://forum.depmap.org/t/how-is-the-of-dependent-cell-lines-a-gene-is-essential-for-calculated/519 "2022-02-04T20:30:45Z")
For example, AAMP is essential in 732/808 cell lines when screened with CRISPR. What dataset do the numbers 732 and 808 come from? Thank you! [Next page](https://forum.depmap.org/tag/portal/1.md?match_all_tags=true&page=1&tags%5B%5D=portal)