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 Rv3306c/amiB1:

update plot	correlation	link to info on gene
Rv3899c/-	(cc=0.4083)	info on Rv3899c/-
Rv2505c/fadD35	(cc=0.4057)	info on Rv2505c/fadD35
Rv2976c/ung	(cc=0.3972)	info on Rv2976c/ung
Rv2453c/mobA	(cc=0.396)	info on Rv2453c/mobA
Rv3585/radA	(cc=0.3943)	info on Rv3585/radA
Rv2658c/-	(cc=0.3934)	info on Rv2658c/-
Rv2029c/pfkB	(cc=0.3902)	info on Rv2029c/pfkB
Rv0969/ctpV	(cc=0.3854)	info on Rv0969/ctpV
Rv1486c/-	(cc=0.3803)	info on Rv1486c/-
Rv0954/-	(cc=0.3801)	info on Rv0954/-

Correlation of Rv3306c/amiB1 with Rv3585/radA

Normalized LFCs for Rv3306c/amiB1:
(description and provenance of datasets)

	Rv3306c/amiB1	Rv3585/radA
Fe_supp_jason_reseq	-0.431	-0.183
low_pH_jason_reseq	-2.453	-0.652
NO_jason_reseq	-0.638	-0.037
B6_jason_reseq	-1.003	-0.008
MHCII_jason_reseq	-0.326	0.374
Isoniazid02	-0.33	0.471
Rifampicin4	0.236	-0.165
Ethambutol3	2.512	1.833
Meropenem3	0.036	1.053
Vancomycin16	-0.698	-0.111
Rv2680_day32	-0.575	0.097
H37Rv_KO_MarP	0.837	-0.017
hypoxia_3wks	-1.459	-0.1
hypoxia_6wks	-0.332	-0.457
glycerol	1.772	0.452
cholesterol	0.668	0.301
AJ	0.0	0.326
Bibs02	0.775	-0.009
Bibs02c	0.747	-0.118
BL6	-1.366	-0.333
BL6a	0.508	-0.23
BXD01	0.252	-0.181
BXD010	-0.47	0.087
BXD011	-1.025	-0.323
BXD03	0.52	0.19
BXD04	-0.676	-0.527
BXD05	0.78	-0.257
BXD06	-0.107	-0.041
BXD07	-0.082	-0.007
BXD08	-0.35	-0.162
BXD09	-0.679	-0.124
CAST	-0.662	-0.035
CCcont	-0.633	-0.932
DS01	0.57	-0.342
DS02	-0.175	0.199
DS04	-0.659	-0.247
DS0c	1.486	0.127
GP01	-0.642	0.305
GP02	-0.402	0.068
GP0c	-0.442	0.54
NOD	-0.088	0.495
NZO	0.354	0.236
PWK	-0.374	0.517
H37Rv_KO_CtpC	-0.235	-0.041
H37Rv_KO_CtpD	-0.075	0.483
H37Rv_KO_Rv1272	-0.557	0.055
H37Rv_KO_SugABC	1.561	0.675
H37Rv_KO_MbtN	-0.172	-0.026
Trans05	0.996	0.547
macrophage_unactivated	0.925	0.401
IL1	0.78	-0.469
Rapamycin	0.899	0.295
Tcell	0.117	0.212
GMCSF	2.688	0.734
IFNab	-0.339	0.52
IFNg	-0.099	0.021
IFNg_GMCSF1	-0.735	0.255
Rv1432_day32	0.498	0.373
Rv1565c_day32	0.565	-0.171
secA2_input	0.178	1.208
delta_Rv3594	-0.968	-0.558
delta_Rv3717	-0.312	-0.415
delta_Rv3811	-0.271	-0.595
delta_Rv0954	-1.796	-0.612
PonA1	0.554	-0.361
EccD1_KO	1.138	-0.053
EspI_KO	0.168	0.151
PE35_KO	0.335	0.274
PPE68_KO	0.873	0.016
glycerol2	0.391	0.263
lignocerate	-0.621	-0.066
oleate	-0.376	0.771
phosphatidylcholine	-0.874	0.42
acetate	-0.554	0.043
glucAc	-1.045	-0.668
Rv0950ko	-1.279	0.76
Rv1096ko	0.522	0.516
Rv3684ko	-1.055	1.074
delta_otsA_trehalose	1.026	0.142