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 Rv1254/-:

update plot	correlation	link to info on gene
Rv2195/qcrA	(cc=0.5168)	info on Rv2195/qcrA
Rv2004c/-	(cc=0.4678)	info on Rv2004c/-
Rv0479c/-	(cc=0.4554)	info on Rv0479c/-
Rv2176/pknL	(cc=0.4476)	info on Rv2176/pknL
Rv0016c/pbpA	(cc=0.4144)	info on Rv0016c/pbpA
Rv0260c/-	(cc=0.3995)	info on Rv0260c/-
Rv3593/lpqF	(cc=0.3839)	info on Rv3593/lpqF
Rv0017c/rodA	(cc=0.3792)	info on Rv0017c/rodA
Rv0589/mce2A	(cc=0.3791)	info on Rv0589/mce2A
Rv1410c/-	(cc=0.3763)	info on Rv1410c/-

Correlation of Rv1254/- with Rv2004c/-

Normalized LFCs for Rv1254/-:
(description and provenance of datasets)

	Rv1254/-	Rv2004c/-
Fe_supp_jason_reseq	0.0	0.655
low_pH_jason_reseq	0.0	0.592
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.526
MHCII_jason_reseq	0.135	2.331
Isoniazid02	-0.183	-1.48
Rifampicin4	-0.341	-1.4
Ethambutol3	-0.32	-1.418
Meropenem3	-0.151	-1.157
Vancomycin16	-0.334	-1.149
Rv2680_day32	0.0	0.608
H37Rv_KO_MarP	-0.684	-0.936
hypoxia_3wks	0.0	0.969
hypoxia_6wks	0.0	0.236
glycerol	0.202	2.262
cholesterol	0.398	1.492
AJ	0.0	0.598
Bibs02	0.0	0.898
Bibs02c	0.574	2.801
BL6	0.0	0.982
BL6a	0.0	2.218
BXD01	0.0	1.666
BXD010	0.0	0.372
BXD011	0.0	0.896
BXD03	0.0	0.592
BXD04	0.0	1.385
BXD05	0.0	1.344
BXD06	0.0	0.995
BXD07	0.0	1.665
BXD08	0.0	2.226
BXD09	0.0	0.958
CAST	0.0	-0.928
CCcont	0.0	1.202
DS01	0.236	2.281
DS02	0.217	1.435
DS04	0.533	2.117
DS0c	0.0	1.788
GP01	0.0	1.367
GP02	0.0	1.104
GP0c	0.0	0.996
NOD	0.0	-0.905
NZO	0.0	-1.065
PWK	0.0	-1.189
H37Rv_KO_CtpC	0.0	1.486
H37Rv_KO_CtpD	0.0	1.305
H37Rv_KO_Rv1272	0.0	2.101
H37Rv_KO_SugABC	0.0	0.94
H37Rv_KO_MbtN	0.0	2.096
Trans05	0.0	2.198
macrophage_unactivated	0.0	1.158
IL1	0.0	-0.872
Rapamycin	0.0	0.114
Tcell	0.0	0.58
GMCSF	0.0	0.38
IFNab	0.0	0.834
IFNg	0.0	0.198
IFNg_GMCSF1	0.0	-0.779
Rv1432_day32	0.0	1.51
Rv1565c_day32	0.218	0.0
secA2_input	-0.412	-0.294
delta_Rv3594	-1.427	-0.171
delta_Rv3717	1.258	0.162
delta_Rv3811	-0.454	-0.123
delta_Rv0954	-1.206	-1.835
PonA1	-1.235	-1.597
EccD1_KO	0.0	-0.414
EspI_KO	0.0	0.485
PE35_KO	0.767	0.572
PPE68_KO	0.442	1.254
glycerol2	0.0	0.671
lignocerate	0.0	0.381
oleate	0.0	-1.184
phosphatidylcholine	0.0	0.203
acetate	0.0	0.106
glucAc	0.0	0.324
Rv0950ko	0.0	-0.087
Rv1096ko	0.0	0.721
Rv3684ko	0.0	0.0
delta_otsA_trehalose	0.133	0.353