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 Rv1885c/-:

update plot	correlation	link to info on gene
Rv1548c/PPE21	(cc=0.5453)	info on Rv1548c/PPE21
Rv2038c/-	(cc=0.4839)	info on Rv2038c/-
Rv3125c/PPE49	(cc=0.4827)	info on Rv3125c/PPE49
Rv2957/-	(cc=0.4605)	info on Rv2957/-
Rv1503c/-	(cc=0.4584)	info on Rv1503c/-
Rv1387/PPE20	(cc=0.4569)	info on Rv1387/PPE20
Rv1917c/PPE34	(cc=0.4569)	info on Rv1917c/PPE34
Rv2809/-	(cc=0.4557)	info on Rv2809/-
Rv1831/-	(cc=0.4544)	info on Rv1831/-
Rv0844c/narL	(cc=0.453)	info on Rv0844c/narL

Correlation of Rv1885c/- with Rv2957/-

Normalized LFCs for Rv1885c/-:
(description and provenance of datasets)

	Rv1885c/-	Rv2957/-
Fe_supp_jason_reseq	-0.204	0.507
low_pH_jason_reseq	-0.37	-0.46
NO_jason_reseq	-0.221	-0.018
B6_jason_reseq	-0.127	0.052
MHCII_jason_reseq	0.283	0.319
Isoniazid02	-0.115	-0.784
Rifampicin4	-0.574	0.417
Ethambutol3	0.129	0.316
Meropenem3	0.028	-0.769
Vancomycin16	-0.732	-0.17
Rv2680_day32	-0.112	0.675
H37Rv_KO_MarP	0.109	0.492
hypoxia_3wks	0.08	-0.12
hypoxia_6wks	-0.263	-0.236
glycerol	-0.252	-0.018
cholesterol	-0.495	-0.17
AJ	0.148	0.171
Bibs02	-0.044	-0.04
Bibs02c	-0.341	0.399
BL6	0.592	0.256
BL6a	-0.125	0.131
BXD01	-0.012	0.434
BXD010	-0.281	0.519
BXD011	0.275	0.322
BXD03	0.223	0.536
BXD04	0.864	0.994
BXD05	0.115	0.11
BXD06	0.0	0.465
BXD07	0.346	0.422
BXD08	0.079	0.268
BXD09	0.09	0.49
CAST	0.01	0.347
CCcont	0.3	0.191
DS01	-0.546	-0.123
DS02	-0.503	0.221
DS04	-0.994	-0.228
DS0c	-0.104	0.358
GP01	-0.087	0.782
GP02	0.512	0.576
GP0c	0.172	0.039
NOD	0.308	0.692
NZO	0.24	-0.402
PWK	0.054	0.395
H37Rv_KO_CtpC	0.418	0.936
H37Rv_KO_CtpD	0.298	0.909
H37Rv_KO_Rv1272	0.94	1.143
H37Rv_KO_SugABC	0.908	0.842
H37Rv_KO_MbtN	0.927	0.76
Trans05	1.173	1.468
macrophage_unactivated	-0.019	0.615
IL1	-0.839	-0.329
Rapamycin	-0.298	-0.307
Tcell	-0.098	-0.476
GMCSF	0.121	-0.869
IFNab	0.157	-0.115
IFNg	-0.08	0.139
IFNg_GMCSF1	0.317	-0.478
Rv1432_day32	0.297	0.01
Rv1565c_day32	-0.608	0.0
secA2_input	-0.282	0.114
delta_Rv3594	0.219	0.061
delta_Rv3717	-0.128	-0.609
delta_Rv3811	0.355	0.0
delta_Rv0954	-0.083	-0.561
PonA1	-0.751	-0.38
EccD1_KO	0.474	0.51
EspI_KO	-0.622	0.853
PE35_KO	0.175	1.103
PPE68_KO	-0.09	0.745
glycerol2	0.233	0.303
lignocerate	0.304	0.247
oleate	-0.238	0.251
phosphatidylcholine	-0.05	0.356
acetate	0.141	-0.318
glucAc	0.311	-0.209
Rv0950ko	0.19	0.666
Rv1096ko	-0.033	-0.344
Rv3684ko	-0.684	0.131
delta_otsA_trehalose	-0.217	-0.462