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 Rv1048c/-:

update plot	correlation	link to info on gene
Rv1288/-	(cc=0.4793)	info on Rv1288/-
Rv1615/-	(cc=0.4253)	info on Rv1615/-
Rv2031c/hspX	(cc=0.4232)	info on Rv2031c/hspX
Rv2888c/amiC	(cc=0.4022)	info on Rv2888c/amiC
Rv1739c/-	(cc=0.3972)	info on Rv1739c/-
Rv0141c/-	(cc=0.3857)	info on Rv0141c/-
Rv2478c/-	(cc=0.3854)	info on Rv2478c/-
Rv0894/-	(cc=0.3843)	info on Rv0894/-
Rv1250/-	(cc=0.3827)	info on Rv1250/-
Rv2725c/hflX	(cc=0.3789)	info on Rv2725c/hflX

Correlation of Rv1048c/- with Rv2478c/-

Normalized LFCs for Rv1048c/-:
(description and provenance of datasets)

	Rv1048c/-	Rv2478c/-
Fe_supp_jason_reseq	-0.44	0.129
low_pH_jason_reseq	0.032	0.599
NO_jason_reseq	0.0	0.483
B6_jason_reseq	-0.363	1.074
MHCII_jason_reseq	-0.108	1.038
Isoniazid02	-0.055	0.458
Rifampicin4	-0.035	0.395
Ethambutol3	0.347	0.567
Meropenem3	1.105	0.334
Vancomycin16	0.114	0.669
Rv2680_day32	0.794	-0.119
H37Rv_KO_MarP	0.349	0.412
hypoxia_3wks	-0.255	0.602
hypoxia_6wks	-0.238	0.257
glycerol	0.274	0.355
cholesterol	0.369	0.827
AJ	0.592	-0.146
Bibs02	-0.098	0.109
Bibs02c	-0.294	1.082
BL6	-0.264	0.062
BL6a	-0.106	0.517
BXD01	0.123	0.0
BXD010	0.266	0.173
BXD011	0.23	-0.855
BXD03	-0.507	0.504
BXD04	-0.231	-0.295
BXD05	0.095	0.453
BXD06	-0.081	0.071
BXD07	0.097	-0.077
BXD08	-0.036	0.019
BXD09	-0.047	-0.025
CAST	0.442	0.813
CCcont	0.397	-0.208
DS01	0.279	0.63
DS02	0.124	-0.758
DS04	0.394	1.19
DS0c	0.083	0.776
GP01	-0.646	-2.067
GP02	-1.245	-0.872
GP0c	-0.758	-1.695
NOD	0.431	0.636
NZO	0.59	0.863
PWK	0.685	0.917
H37Rv_KO_CtpC	-0.58	-1.243
H37Rv_KO_CtpD	-0.267	0.842
H37Rv_KO_Rv1272	0.438	-0.395
H37Rv_KO_SugABC	0.326	-0.659
H37Rv_KO_MbtN	0.457	1.059
Trans05	0.347	-0.22
macrophage_unactivated	0.773	0.23
IL1	-0.575	-0.246
Rapamycin	-0.377	-0.562
Tcell	-0.104	0.417
GMCSF	0.298	1.296
IFNab	0.602	-0.115
IFNg	-0.029	-0.313
IFNg_GMCSF1	1.254	0.584
Rv1432_day32	0.644	0.389
Rv1565c_day32	1.99	0.851
secA2_input	-0.67	0.185
delta_Rv3594	0.43	0.821
delta_Rv3717	0.065	0.143
delta_Rv3811	0.503	0.317
delta_Rv0954	0.277	0.173
PonA1	0.09	-0.563
EccD1_KO	0.52	-0.204
EspI_KO	0.473	-0.445
PE35_KO	0.312	-0.298
PPE68_KO	0.397	-0.054
glycerol2	0.245	0.164
lignocerate	-0.192	0.089
oleate	0.428	0.544
phosphatidylcholine	0.106	0.392
acetate	0.15	-0.444
glucAc	-0.06	-0.468
Rv0950ko	-0.121	-0.88
Rv1096ko	-0.498	-1.218
Rv3684ko	-0.052	-0.884
delta_otsA_trehalose	-0.215	-0.164