differentially expressed gene

Question

[haribioinfo05]

dear sir,

how to find differentially expressed gene?

ID               adj.P.Val    P.Value      t            B            logFC        Gene.symbol
ILMN_1745607     3.50E-57     7.40E-62     38.6646      128.3397     8.106586     A2M
ILMN_1752755     4.38E-44     1.85E-48     27.56745     99.19733     7.387721     VWF
ILMN_2157441     8.54E-43     6.70E-47     26.46402     95.74092     7.017251     HLA-DRA
ILMN_1709162     8.54E-43     7.22E-47     -26.4416     95.66943     -3.17902     SHCBP1
ILMN_1761733     9.81E-43     1.04E-46     26.33227     95.32021     6.422425     HLA-DMB
ILMN_3250257     2.40E-42     3.04E-46     26.00918     94.28114     4.908232     ACVRL1
ILMN_1704730     6.44E-42     9.53E-46     25.66985     93.17846     6.000549     CD93
ILMN_1693826     5.49E-40     9.28E-44     24.34132     88.74547     5.449931     HAVCR2
ILMN_2141482     7.72E-40     1.47E-43     24.21095     88.30028     5.984509     SERPINF1
ILMN_1778977     1.07E-39     2.25E-43     24.08983     87.88503     6.99495      TYROBP
ILMN_1772218     1.30E-39     3.02E-43     24.00719     87.60076     7.480757     HLA-DPA1

[Michael]

Dear Hari, please do not address the community as "dear sir", instead of trying to be polite, try to give more background information, that would be real courtesy. Differentially expressed genes are generally indicated by low p-values or low adjusted p.values in tests for differential expression.

[Manvendra Singh]

hari, usage of sir or ma'am is funny here, I was also doing the same in India, becomes habit, changed it.

Your logFC column is differentially expressed value, coupled with adj.P.Value which false discovery rate (fdr), try not to consider genes which has fdr more than 5%

If logFC is positive then it's up-regulated otherwise down-regulated

hth sir :) :)

[haribioinfo05]

thank sir...