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 Rv2712c/-:

update plot	correlation	link to info on gene
Rv3906c/-	(cc=0.5133)	info on Rv3906c/-
Rv0325/-	(cc=0.506)	info on Rv0325/-
Rv2020c/-	(cc=0.4764)	info on Rv2020c/-
Rv1688/mpg	(cc=0.4674)	info on Rv1688/mpg
Rv2238c/ahpE	(cc=0.4601)	info on Rv2238c/ahpE
Rv2629/-	(cc=0.4594)	info on Rv2629/-
Rv0735/sigL	(cc=0.4409)	info on Rv0735/sigL
Rv0747/PE_PGRS10	(cc=0.4391)	info on Rv0747/PE_PGRS10
Rv1378c/-	(cc=0.4338)	info on Rv1378c/-
Rv1442/bisC	(cc=0.4318)	info on Rv1442/bisC

Correlation of Rv2712c/- with Rv1442/bisC

Normalized LFCs for Rv2712c/-:
(description and provenance of datasets)

	Rv2712c/-	Rv1442/bisC
Fe_supp_jason_reseq	-0.046	0.137
low_pH_jason_reseq	0.4	-0.673
NO_jason_reseq	0.407	-0.431
B6_jason_reseq	-0.54	0.363
MHCII_jason_reseq	0.617	0.584
Isoniazid02	1.487	0.316
Rifampicin4	0.157	0.341
Ethambutol3	0.969	0.253
Meropenem3	0.424	0.391
Vancomycin16	0.393	0.385
Rv2680_day32	-0.083	0.356
H37Rv_KO_MarP	-0.697	0.028
hypoxia_3wks	-0.395	0.0
hypoxia_6wks	0.207	0.299
glycerol	0.619	0.53
cholesterol	0.377	0.312
AJ	0.469	0.207
Bibs02	0.499	-0.158
Bibs02c	-0.482	0.286
BL6	-0.561	-0.101
BL6a	-0.677	-0.059
BXD01	0.042	-0.045
BXD010	-0.847	-0.277
BXD011	-0.236	-0.315
BXD03	-0.403	-0.146
BXD04	-0.368	0.024
BXD05	-0.132	-0.267
BXD06	-0.136	-0.242
BXD07	-0.231	-0.476
BXD08	-0.171	-0.241
BXD09	-0.144	-0.391
CAST	0.01	-0.164
CCcont	-0.553	-0.09
DS01	0.228	0.303
DS02	0.38	0.336
DS04	-0.287	0.426
DS0c	-0.321	0.561
GP01	-0.631	0.127
GP02	0.535	0.572
GP0c	0.077	-0.258
NOD	-0.189	0.308
NZO	0.342	-0.02
PWK	0.233	-0.108
H37Rv_KO_CtpC	-0.718	-0.391
H37Rv_KO_CtpD	0.462	0.054
H37Rv_KO_Rv1272	-0.499	-0.967
H37Rv_KO_SugABC	0.594	0.482
H37Rv_KO_MbtN	0.382	0.27
Trans05	-0.237	-0.504
macrophage_unactivated	-0.095	0.208
IL1	0.154	0.448
Rapamycin	-0.31	0.0
Tcell	-0.225	0.342
GMCSF	0.378	0.438
IFNab	0.514	0.366
IFNg	-0.102	0.302
IFNg_GMCSF1	0.321	0.402
Rv1432_day32	0.094	0.018
Rv1565c_day32	0.341	0.742
secA2_input	-0.351	-0.528
delta_Rv3594	0.207	-0.434
delta_Rv3717	-0.457	-0.077
delta_Rv3811	-0.055	-0.391
delta_Rv0954	-0.479	-0.261
PonA1	-0.196	-0.113
EccD1_KO	0.526	-0.158
EspI_KO	0.365	-0.607
PE35_KO	-0.551	-0.111
PPE68_KO	-0.378	0.0
glycerol2	0.161	0.716
lignocerate	0.622	1.276
oleate	0.736	0.438
phosphatidylcholine	0.655	1.056
acetate	0.336	0.721
glucAc	0.187	0.793
Rv0950ko	0.214	0.054
Rv1096ko	0.042	0.347
Rv3684ko	0.072	0.0
delta_otsA_trehalose	0.576	0.348