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 Rv3115/-

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

	Rv1396c/PE_PGRS25	Rv3115/-
Fe_supp_jason_reseq	-1.14	-0.863
low_pH_jason_reseq	-0.545	-0.112
NO_jason_reseq	-1.701	-0.454
B6_jason_reseq	-1.043	-0.205
MHCII_jason_reseq	-0.633	-0.145
Isoniazid02	-1.352	-1.094
Rifampicin4	0.921	0.263
Ethambutol3	-0.045	-0.495
Meropenem3	-1.155	-0.155
Vancomycin16	-0.249	-0.743
Rv2680_day32	-0.48	0.457
H37Rv_KO_MarP	0.161	-0.299
hypoxia_3wks	-0.116	0.315
hypoxia_6wks	-0.896	-0.631
glycerol	1.369	0.022
cholesterol	1.175	-0.27
AJ	2.575	0.847
Bibs02	1.734	0.864
Bibs02c	1.585	1.378
BL6	0.257	-0.082
BL6a	0.809	0.839
BXD01	0.987	0.57
BXD010	0.562	0.409
BXD011	0.419	0.247
BXD03	0.352	0.737
BXD04	0.486	0.617
BXD05	0.975	0.724
BXD06	-0.463	0.546
BXD07	0.818	0.691
BXD08	1.008	0.35
BXD09	0.919	0.482
CAST	0.941	0.789
CCcont	0.515	0.048
DS01	0.395	0.416
DS02	0.821	0.922
DS04	0.325	0.679
DS0c	0.234	0.459
GP01	0.89	0.242
GP02	1.607	0.437
GP0c	1.185	0.252
NOD	0.0	0.752
NZO	0.905	0.351
PWK	0.831	0.516
H37Rv_KO_CtpC	1.369	0.916
H37Rv_KO_CtpD	2.165	0.384
H37Rv_KO_Rv1272	0.834	0.776
H37Rv_KO_SugABC	0.845	0.918
H37Rv_KO_MbtN	1.015	0.114
Trans05	0.408	0.918
macrophage_unactivated	-0.145	0.552
IL1	-0.089	0.068
Rapamycin	-1.034	-0.221
Tcell	0.0	-1.303
GMCSF	-0.121	-0.319
IFNab	-0.429	-0.366
IFNg	-0.901	-0.291
IFNg_GMCSF1	0.138	-0.148
Rv1432_day32	0.553	-0.083
Rv1565c_day32	0.257	0.357
secA2_input	-0.601	-0.225
delta_Rv3594	1.319	0.246
delta_Rv3717	0.32	-0.101
delta_Rv3811	0.697	0.068
delta_Rv0954	-0.092	0.116
PonA1	0.21	-0.426
EccD1_KO	0.303	-0.23
EspI_KO	1.3	0.516
PE35_KO	0.933	0.7
PPE68_KO	0.403	-0.045
glycerol2	-0.479	-1.113
lignocerate	-0.897	-0.76
oleate	0.465	-0.885
phosphatidylcholine	-0.342	-0.713
acetate	0.0	1.172
glucAc	-0.734	0.091
Rv0950ko	-0.437	-0.362
Rv1096ko	-1.644	-0.76
Rv3684ko	-0.416	-1.15
delta_otsA_trehalose	-0.525	-0.404