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 Rv2228c/-:

update plot	correlation	link to info on gene
Rv2973c/recG	(cc=0.4745)	info on Rv2973c/recG
Rv1067c/PE_PGRS19	(cc=0.474)	info on Rv1067c/PE_PGRS19
Rv2401/-	(cc=0.4534)	info on Rv2401/-
Rv2976c/ung	(cc=0.4413)	info on Rv2976c/ung
Rv2169c/-	(cc=0.4359)	info on Rv2169c/-
Rv0003/recF	(cc=0.4274)	info on Rv0003/recF
Rv3262/fbiB	(cc=0.425)	info on Rv3262/fbiB
Rv0778/cyp126	(cc=0.4213)	info on Rv0778/cyp126
Rv3674c/nth	(cc=0.4195)	info on Rv3674c/nth
Rv2922c/smc	(cc=0.4175)	info on Rv2922c/smc

Correlation of Rv2228c/- with Rv0778/cyp126

Normalized LFCs for Rv2228c/-:
(description and provenance of datasets)

	Rv2228c/-	Rv0778/cyp126
Fe_supp_jason_reseq	0.268	2.014
low_pH_jason_reseq	-1.134	-0.571
NO_jason_reseq	0.0	-0.651
B6_jason_reseq	1.206	0.523
MHCII_jason_reseq	0.315	0.706
Isoniazid02	-0.49	-0.525
Rifampicin4	-0.523	0.157
Ethambutol3	-0.153	-0.403
Meropenem3	0.138	0.298
Vancomycin16	-0.512	0.154
Rv2680_day32	0.0	0.508
H37Rv_KO_MarP	-1.065	-0.423
hypoxia_3wks	-0.427	0.534
hypoxia_6wks	-0.223	-0.021
glycerol	2.07	0.736
cholesterol	0.159	0.449
AJ	0.0	0.824
Bibs02	-0.109	0.174
Bibs02c	-0.887	0.246
BL6	-0.074	-0.148
BL6a	-0.377	0.756
BXD01	0.552	0.734
BXD010	0.206	0.959
BXD011	-0.335	0.899
BXD03	0.0	0.561
BXD04	0.932	1.184
BXD05	-0.256	0.862
BXD06	0.513	0.836
BXD07	0.0	0.79
BXD08	-0.35	0.618
BXD09	0.596	0.696
CAST	-0.284	0.756
CCcont	0.898	-0.056
DS01	1.641	0.921
DS02	1.638	1.078
DS04	-0.115	0.207
DS0c	1.867	0.919
GP01	-0.607	-0.265
GP02	-0.353	-0.021
GP0c	-0.16	0.665
NOD	0.127	1.642
NZO	0.994	0.581
PWK	0.412	0.715
H37Rv_KO_CtpC	0.0	0.916
H37Rv_KO_CtpD	0.0	1.194
H37Rv_KO_Rv1272	-0.084	-0.269
H37Rv_KO_SugABC	-0.509	1.345
H37Rv_KO_MbtN	-0.061	0.918
Trans05	-0.444	0.278
macrophage_unactivated	0.83	1.042
IL1	-0.611	0.0
Rapamycin	-0.307	0.341
Tcell	0.59	0.437
GMCSF	0.478	0.591
IFNab	0.0	0.0
IFNg	-0.551	1.04
IFNg_GMCSF1	0.0	0.566
Rv1432_day32	0.0	-0.624
Rv1565c_day32	0.0	-0.347
secA2_input	-1.021	0.23
delta_Rv3594	0.47	0.72
delta_Rv3717	-0.992	-0.162
delta_Rv3811	-1.172	0.744
delta_Rv0954	-1.499	0.549
PonA1	-0.286	0.753
EccD1_KO	0.178	0.52
EspI_KO	0.0	0.893
PE35_KO	-0.166	0.983
PPE68_KO	0.813	0.841
glycerol2	-1.202	-0.13
lignocerate	-1.55	-0.614
oleate	-0.345	0.39
phosphatidylcholine	-0.803	0.088
acetate	-0.663	-0.748
glucAc	-1.831	-1.202
Rv0950ko	0.172	0.329
Rv1096ko	-0.555	0.633
Rv3684ko	-0.393	0.121
delta_otsA_trehalose	0.564	-1.184