mitranscriptome

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Welcome to the general user group for the MiTranscriptome study. The MiTranscriptome is an ab initio reconstruction of the human transcriptome from thousands of RNA-Seq samples from human tumors, benign tissues, and cell lines. The public forum serves as a way for us to support the study and online portal. Please post your feature requests and any issues you encounter here. Results from the study can be accessed via the online portal at: http://mitranscriptome.org. The MiTranscriptome paper has been published by Nature Genetics (dx.doi.org/10.1038/ng.3192).

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You Chen, Lilia Estrada2

12/6/22

Not able to access the website

I am having the same problem. I am not able to access to the website. I want to download some

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Not able to access the website

I am having the same problem. I am not able to access to the website. I want to download some

12/6/22

7/3/20

Number of transcripts vs number of genes

Would you please tell me the exact number of lncRNA transcripts vs lncRNA genes of your database?

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Number of transcripts vs number of genes

Would you please tell me the exact number of lncRNA transcripts vs lncRNA genes of your database?

7/3/20

guang...@gmail.com

6/5/20

expression of G088966

Could you please provide the expression data of each transcript of G088966 in prostate cancer? It is

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expression of G088966

Could you please provide the expression data of each transcript of G088966 in prostate cancer? It is

6/5/20

bkal...@gmail.com

5/26/20

Hello, I would like to use miTranscriptome, but need to use Hg38. I have been trying to lift over

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Hello, I would like to use miTranscriptome, but need to use Hg38. I have been trying to lift over

5/26/20

Rachael Kuintzle, … daniel Gautheret10

5/13/19

Previously annotated gene symbols

Dear all, In line with this thread: can I get the equivalence table between Mitranscriptome gene_id

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Previously annotated gene symbols

Dear all, In line with this thread: can I get the equivalence table between Mitranscriptome gene_id

5/13/19

Gireesh K. Bogu, … yuanzhi...@gmail.com4

11/20/18

Hi, Gireesh did you run SSEA correctly and get expected results ?

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Hi, Gireesh did you run SSEA correctly and get expected results ?

11/20/18

yuanzhi...@gmail.com

11/17/18

SSEA manuscript and input data

Hi, Is there a manuscript for SSEA? how SSEA know which sample is cancer or normal ? Can you fork a

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SSEA manuscript and input data

Hi, Is there a manuscript for SSEA? how SSEA know which sample is cancer or normal ? Can you fork a

11/17/18

jlerg...@gmail.com

7/23/18

expression of an isoform: T291020

Please, it would be great if you could provide in which tissues the transcript T291020 is expressed.

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expression of an isoform: T291020

Please, it would be great if you could provide in which tissues the transcript T291020 is expressed.

7/23/18

Matthew Cserhati

6/4/18

lncRNA data from TCGA

Hello all, I see that the data on oncolnc.org is RNA-seq expression data from the TCGA database.

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lncRNA data from TCGA

Hello all, I see that the data on oncolnc.org is RNA-seq expression data from the TCGA database.

6/4/18

dvelm...@gmail.com, mendez....@gmail.com2

11/28/17

MiTranscriptome GTF based on GRCh38 genome assembly

Hello, I am also interested in working with MiTranscriptome mapped on GRCh38. Is there a plan for a

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MiTranscriptome GTF based on GRCh38 genome assembly

Hello, I am also interested in working with MiTranscriptome mapped on GRCh38. Is there a plan for a

11/28/17

6/16/17

How to download list of lncRNA names associated to cancer?

Dear Authors, Thanks for this wonderful resource. I was wondering if their was any way to download

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How to download list of lncRNA names associated to cancer?

Dear Authors, Thanks for this wonderful resource. I was wondering if their was any way to download

6/16/17

jlerg...@gmail.com

3/21/17

T291020 transcript tissue expression

Hi, it would be great if you could provide in which tissues the transcript T291020 is expressed. It

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T291020 transcript tissue expression

Hi, it would be great if you could provide in which tissues the transcript T291020 is expressed. It

3/21/17

3/14/17

Hi I am trying to exctract expression data regaridng these two lncRNAs in different trypes of cancer:

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Hi I am trying to exctract expression data regaridng these two lncRNAs in different trypes of cancer:

3/14/17

wln...@gmail.com

2/28/17

download the names of selected lncRNAs

Hi, I used http://mitranscriptome.org/, and got 471 lncRNAs for Melanoma tissue type. I did not find

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download the names of selected lncRNAs

Hi, I used http://mitranscriptome.org/, and got 471 lncRNAs for Melanoma tissue type. I did not find

2/28/17

jlerg...@gmail.com, Yashar Niknafs5

1/10/17

expression of some lncRNAs ; tissues

Please, it would be great if you could provide in which tissues the transcript T291020 is expressed.

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expression of some lncRNAs ; tissues

Please, it would be great if you could provide in which tissues the transcript T291020 is expressed.

1/10/17

jobv...@gmail.com

1/5/17

Full MiTranscriptome dataset

Dear Yashar (and others), For a project concerning the expression patterns of genome-wide transcripts

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Full MiTranscriptome dataset

Dear Yashar (and others), For a project concerning the expression patterns of genome-wide transcripts

1/5/17

ygi...@gmail.com, Yashar Niknafs2

12/6/16

about the fpkm_mean fpkm_95 and fpkm_99

Hello, To answer your questions. the percentile values were calculated by identifying the Nth

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about the fpkm_mean fpkm_95 and fpkm_99

Hello, To answer your questions. the percentile values were calculated by identifying the Nth

12/6/16

jcohan, Yashar Niknafs2

12/6/16

get expression values of all genes (lncRNAs and protein-coding genes)

Hello, A file like this is not readily accessible on the site in its current form. We are sorry about

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get expression values of all genes (lncRNAs and protein-coding genes)

Hello, A file like this is not readily accessible on the site in its current form. We are sorry about

12/6/16

Hua Zhong, … Yashar Niknafs5

7/19/16

Lots of exons in Mitranscriptome file couldn't be found in Enssembl browser.

Hello Leonie, So the emsembl annotaton of a gene is a curated structure for the gene. The

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Lots of exons in Mitranscriptome file couldn't be found in Enssembl browser.

Hello Leonie, So the emsembl annotaton of a gene is a curated structure for the gene. The

7/19/16

Brendan Miller, … Yashar Niknafs7

7/13/16

file of highest differentially expressed lncRNA with cancer/lineage and tissue information

No problem. Look here: https://groups.google.com/d/msg/mitranscriptome/hpxMMwo5ysM/L9rg4yVvBQAJ -

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file of highest differentially expressed lncRNA with cancer/lineage and tissue information

No problem. Look here: https://groups.google.com/d/msg/mitranscriptome/hpxMMwo5ysM/L9rg4yVvBQAJ -

7/13/16

Ami Rav, Yashar Niknafs2

7/11/16

search using Assembly Transcript ID (or Assembly Gene ID)

Hello, In the attached file, you will see the metadata for all of the transcripts found on the

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search using Assembly Transcript ID (or Assembly Gene ID)

Hello, In the attached file, you will see the metadata for all of the transcripts found on the

7/11/16

indran...@gmail.com

6/16/16

LncRNA Expression data Request

Hello, In one of our project, we wanted to analyze lncRNAs in TCGA cohort data. I know you have

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LncRNA Expression data Request

Hello, In one of our project, we wanted to analyze lncRNAs in TCGA cohort data. I know you have

6/16/16

samha...@gmail.com, Yashar Niknafs3

6/16/16

Strand information in GTF

Hi Yashar, Thank you very much for your quick response and for your explanation. I think for now we

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Strand information in GTF

Hi Yashar, Thank you very much for your quick response and for your explanation. I think for now we

6/16/16

lsp0...@gmail.com, … Margherita7

6/14/16

release all expression values of lncRNAs and protein-coding genes

Dear Yashar, Thank you for your message. The idea was to get the information across all the tissues

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release all expression values of lncRNAs and protein-coding genes

Dear Yashar, Thank you for your message. The idea was to get the information across all the tissues

6/14/16

indran...@gmail.com, Yashar Niknafs2

5/4/16

GTF & FPKM expr file

Hello, In the GTF file, there is an attribute "transcript_id" that will match up with the

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GTF & FPKM expr file

Hello, In the GTF file, there is an attribute "transcript_id" that will match up with the

5/4/16

Azim dehghani Amirabad, Yashar Niknafs2

5/4/16

When is the release date of new version?

Hello, We are shooting for a mid-to-late summer release. In the mean time if you have any lncRNAs you

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When is the release date of new version?

Hello, We are shooting for a mid-to-late summer release. In the mean time if you have any lncRNAs you

5/4/16

xypan...@gmail.com, … Yashar Niknafs3

5/4/16

Tissue information in mitranscriptome.expr.fpkm.tsv.gz

Hello, There is also a "Library information" file in the downloads tab of the site that

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Tissue information in mitranscriptome.expr.fpkm.tsv.gz

Hello, There is also a "Library information" file in the downloads tab of the site that

5/4/16

daniel Gautheret, … Yashar Niknafs4

5/4/16

Genome assembly version

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Genome assembly version

5/4/16

Mathijs, Yashar Niknafs2

5/4/16

How can I couple transcript IDs with tissue type?

Hello Mathijs, So to answer your question, there isn't a hard and fast "tissue type"

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How can I couple transcript IDs with tissue type?

Hello Mathijs, So to answer your question, there isn't a hard and fast "tissue type"

5/4/16

2/26/16

Very interactive and career oriented Ab initio training

Bytes Online Training is the leading training company occupied in provided that on a range of

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Very interactive and career oriented Ab initio training

Bytes Online Training is the leading training company occupied in provided that on a range of

2/26/16

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