TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1754c/-:

update plot	correlation	link to info on gene
Rv2161c/-	(cc=0.4631)	info on Rv2161c/-
Rv1785c/cyp143	(cc=0.4129)	info on Rv1785c/cyp143
Rv0742/PE_PGRS8	(cc=0.4082)	info on Rv0742/PE_PGRS8
Rv2500c/fadE19	(cc=0.408)	info on Rv2500c/fadE19
Rv1584c/-	(cc=0.4066)	info on Rv1584c/-
Rv3160c/-	(cc=0.4003)	info on Rv3160c/-
Rv3826/fadD23	(cc=0.3982)	info on Rv3826/fadD23
Rv3158/nuoN	(cc=0.3958)	info on Rv3158/nuoN
Rv1787/PPE25	(cc=0.385)	info on Rv1787/PPE25
Rv1770/-	(cc=0.3772)	info on Rv1770/-

Correlation of Rv1754c/- with Rv1787/PPE25

Normalized LFCs for Rv1754c/-:
(description and provenance of datasets)

	Rv1754c/-	Rv1787/PPE25
Fe_supp_jason_reseq	0.011	-0.851
low_pH_jason_reseq	-0.442	-1.655
NO_jason_reseq	0.055	-0.042
B6_jason_reseq	-0.284	-1.404
MHCII_jason_reseq	-0.283	-1.249
Isoniazid02	0.69	0.308
Rifampicin4	3.344	0.842
Ethambutol3	0.664	0.372
Meropenem3	-0.374	0.574
Vancomycin16	1.73	-0.398
Rv2680_day32	0.183	0.419
H37Rv_KO_MarP	0.212	-0.1
hypoxia_3wks	-0.674	0.267
hypoxia_6wks	-0.207	0.0
glycerol	0.164	0.041
cholesterol	0.338	-0.952
AJ	0.378	0.492
Bibs02	-0.101	0.221
Bibs02c	0.327	-0.029
BL6	0.366	0.067
BL6a	0.425	0.158
BXD01	0.856	0.369
BXD010	0.433	0.332
BXD011	1.18	0.413
BXD03	0.443	0.551
BXD04	0.524	0.157
BXD05	0.166	0.695
BXD06	0.286	0.237
BXD07	0.468	0.622
BXD08	0.699	0.401
BXD09	0.134	0.435
CAST	-0.362	-0.008
CCcont	0.497	0.056
DS01	0.226	-0.476
DS02	0.145	0.022
DS04	-0.091	0.559
DS0c	0.424	0.044
GP01	0.408	0.916
GP02	1.011	1.683
GP0c	0.426	0.736
NOD	0.454	-0.039
NZO	-0.227	0.342
PWK	-1.248	0.337
H37Rv_KO_CtpC	0.654	0.718
H37Rv_KO_CtpD	0.838	0.635
H37Rv_KO_Rv1272	0.794	0.769
H37Rv_KO_SugABC	0.384	0.657
H37Rv_KO_MbtN	0.113	0.831
Trans05	1.442	0.971
macrophage_unactivated	0.376	0.41
IL1	0.439	0.501
Rapamycin	0.157	-0.021
Tcell	0.834	0.632
GMCSF	0.187	1.009
IFNab	0.302	-0.577
IFNg	0.369	1.013
IFNg_GMCSF1	0.192	0.886
Rv1432_day32	-0.724	0.394
Rv1565c_day32	-1.987	-0.581
secA2_input	-0.553	0.504
delta_Rv3594	-0.422	-0.171
delta_Rv3717	-0.17	-0.298
delta_Rv3811	0.0	-0.228
delta_Rv0954	0.036	-0.238
PonA1	-0.638	-0.602
EccD1_KO	0.0	-0.043
EspI_KO	-0.145	0.371
PE35_KO	0.341	0.327
PPE68_KO	0.179	-0.186
glycerol2	0.196	0.017
lignocerate	0.613	-0.3
oleate	0.179	0.517
phosphatidylcholine	0.521	0.353
acetate	0.485	-0.229
glucAc	0.372	-0.284
Rv0950ko	-0.178	0.323
Rv1096ko	-0.489	-0.688
Rv3684ko	-0.043	-0.793
delta_otsA_trehalose	1.21	0.776