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 Rv1396c/PE_PGRS25:

update plot	correlation	link to info on gene
Rv3115/-	(cc=0.6254)	info on Rv3115/-
Rv2479c/-	(cc=0.6214)	info on Rv2479c/-
Rv2512c/-	(cc=0.6208)	info on Rv2512c/-
Rv2106/-	(cc=0.6207)	info on Rv2106/-
Rv2814c/-	(cc=0.6204)	info on Rv2814c/-
Rv3475/-	(cc=0.6189)	info on Rv3475/-
Rv1047/-	(cc=0.6106)	info on Rv1047/-
Rv2279/-	(cc=0.6061)	info on Rv2279/-
Rv1369c/-	(cc=0.6048)	info on Rv1369c/-
Rv1756c/-	(cc=0.6034)	info on Rv1756c/-

Correlation of Rv1396c/PE_PGRS25 with Rv3475/-

Normalized LFCs for Rv1396c/PE_PGRS25:
(description and provenance of datasets)

	Rv1396c/PE_PGRS25	Rv3475/-
Fe_supp_jason_reseq	-1.14	-0.456
low_pH_jason_reseq	-0.545	-0.413
NO_jason_reseq	-1.701	0.179
B6_jason_reseq	-1.043	-0.671
MHCII_jason_reseq	-0.633	-0.15
Isoniazid02	-1.352	0.0
Rifampicin4	0.921	0.942
Ethambutol3	-0.045	0.591
Meropenem3	-1.155	-0.201
Vancomycin16	-0.249	0.117
Rv2680_day32	-0.48	0.249
H37Rv_KO_MarP	0.161	-0.253
hypoxia_3wks	-0.116	0.439
hypoxia_6wks	-0.896	0.161
glycerol	1.369	-0.549
cholesterol	1.175	0.198
AJ	2.575	1.348
Bibs02	1.734	1.098
Bibs02c	1.585	1.491
BL6	0.257	0.014
BL6a	0.809	0.897
BXD01	0.987	0.73
BXD010	0.562	0.761
BXD011	0.419	0.827
BXD03	0.352	0.847
BXD04	0.486	0.477
BXD05	0.975	1.002
BXD06	-0.463	0.547
BXD07	0.818	0.881
BXD08	1.008	0.53
BXD09	0.919	0.673
CAST	0.941	1.17
CCcont	0.515	-0.026
DS01	0.395	0.922
DS02	0.821	0.934
DS04	0.325	1.107
DS0c	0.234	1.039
GP01	0.89	1.169
GP02	1.607	1.477
GP0c	1.185	0.835
NOD	0.0	1.334
NZO	0.905	1.006
PWK	0.831	1.216
H37Rv_KO_CtpC	1.369	0.741
H37Rv_KO_CtpD	2.165	0.814
H37Rv_KO_Rv1272	0.834	0.492
H37Rv_KO_SugABC	0.845	0.875
H37Rv_KO_MbtN	1.015	0.553
Trans05	0.408	0.771
macrophage_unactivated	-0.145	-0.95
IL1	-0.089	-0.217
Rapamycin	-1.034	-0.638
Tcell	0.0	-0.981
GMCSF	-0.121	-0.103
IFNab	-0.429	-0.674
IFNg	-0.901	-0.42
IFNg_GMCSF1	0.138	-0.295
Rv1432_day32	0.553	0.837
Rv1565c_day32	0.257	0.167
secA2_input	-0.601	0.072
delta_Rv3594	1.319	-0.066
delta_Rv3717	0.32	-0.109
delta_Rv3811	0.697	-0.156
delta_Rv0954	-0.092	0.41
PonA1	0.21	0.122
EccD1_KO	0.303	0.155
EspI_KO	1.3	1.184
PE35_KO	0.933	1.05
PPE68_KO	0.403	0.819
glycerol2	-0.479	-0.771
lignocerate	-0.897	-0.728
oleate	0.465	-0.767
phosphatidylcholine	-0.342	-0.718
acetate	0.0	0.0
glucAc	-0.734	-0.168
Rv0950ko	-0.437	-0.178
Rv1096ko	-1.644	0.057
Rv3684ko	-0.416	-0.783
delta_otsA_trehalose	-0.525	0.549