Connectivity Map: "invalid tag files: down tags: probe '211851_X_AT' invalid, not found in database"

Question

[adropofilm]

Hi everyone,

I am new to connectivity map. I am trying to conduct a quick query of down regulated genes, however, I am running into several problems. I am not sure where to start, as I am new to working with bioinformatics tools. I looked into the help link, however it did not help me much.

• Are two files REQUIRED for quick search to work? Do I HAVE to upload an up-regulated grp file in addition to the down-regulated grp file that I wanted to run a query on?
• I tried to upload both an up-regulated and down-regulated list, but the following is an excerpt from the error message was returned:

invalid tag files:
    down tags: probe '211851_X_AT' invalid, not found in database
    down tags: probe '41324_G_AT' invalid, not found in database
    down tags: probe 'X95152_RNA1_AT' invalid, not found in database
    down tags: probe '34715_AT' invalid, not found in database

This is really overwhelming, and I would like any insight that I can get.

Thank you all in advance!

P.S.

This is what is in the down-regulated.grp file I uploaded:

HS.34012.1.S1_3P_AT
208368_S_AT
214727_PM_AT
1989_AT
G4502450_3P_A_AT
1990_G_AT
214727_AT
208368_PM_S_AT
208368_3P_S_AT
1503_AT
58994_3P_AT
207083_S_AT
HS.181780.1.S1_3P_S_AT
222137_PM_AT
63759_R_AT
207083_PM_S_AT
221888_PM_AT
58994_AT
G8923216_3P_A_AT
67178_AT
RC_N27334_AT
HS.181780.2.S1_3P_AT
60486_AT
222137_AT
4854074C_3P_S_AT
58994_PM_AT
211851_X_AT

Answer 1

[Zhilong Jia]

Only probes from HG-U133A are supported by CMap. Both up and down-regulated probes are necessary.

You can get help from http://www.connectivitymap.org/cmap/help_getting_started_linkified.jsp and http://www.connectivitymap.org/cmap/help_topics_frames.jsp?topic=signature

[adropofilm]

Thank you! It ended up working! :)