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 Rv1949c/-:

update plot	correlation	link to info on gene
Rv0403c/mmpS1	(cc=0.6195)	info on Rv0403c/mmpS1
Rv1521/fadD25	(cc=0.5944)	info on Rv1521/fadD25
Rv1984c/cfp21	(cc=0.5857)	info on Rv1984c/cfp21
Rv2435c/-	(cc=0.577)	info on Rv2435c/-
Rv1871c/-	(cc=0.5509)	info on Rv1871c/-
Rv1215c/-	(cc=0.5463)	info on Rv1215c/-
Rv1861/-	(cc=0.5442)	info on Rv1861/-
Rv1504c/-	(cc=0.5404)	info on Rv1504c/-
Rv2545/vapB18	(cc=0.5051)	info on Rv2545/vapB18
Rv2957/-	(cc=0.5029)	info on Rv2957/-

Correlation of Rv1949c/- with Rv2957/-

Normalized LFCs for Rv1949c/-:
(description and provenance of datasets)

	Rv1949c/-	Rv2957/-
Fe_supp_jason_reseq	0.311	0.507
low_pH_jason_reseq	-0.689	-0.46
NO_jason_reseq	0.239	-0.018
B6_jason_reseq	-0.692	0.052
MHCII_jason_reseq	-0.969	0.319
Isoniazid02	-0.113	-0.784
Rifampicin4	-0.011	0.417
Ethambutol3	0.047	0.316
Meropenem3	0.629	-0.769
Vancomycin16	-0.377	-0.17
Rv2680_day32	0.057	0.675
H37Rv_KO_MarP	0.48	0.492
hypoxia_3wks	0.303	-0.12
hypoxia_6wks	-0.547	-0.236
glycerol	-0.888	-0.018
cholesterol	0.519	-0.17
AJ	-0.044	0.171
Bibs02	0.258	-0.04
Bibs02c	-0.341	0.399
BL6	-0.195	0.256
BL6a	-0.142	0.131
BXD01	0.438	0.434
BXD010	-0.041	0.519
BXD011	0.194	0.322
BXD03	0.242	0.536
BXD04	0.926	0.994
BXD05	0.283	0.11
BXD06	0.033	0.465
BXD07	0.226	0.422
BXD08	0.742	0.268
BXD09	0.274	0.49
CAST	0.085	0.347
CCcont	-0.573	0.191
DS01	0.074	-0.123
DS02	0.041	0.221
DS04	-0.675	-0.228
DS0c	-0.402	0.358
GP01	0.819	0.782
GP02	0.762	0.576
GP0c	-0.221	0.039
NOD	-0.072	0.692
NZO	0.038	-0.402
PWK	-0.013	0.395
H37Rv_KO_CtpC	0.887	0.936
H37Rv_KO_CtpD	0.158	0.909
H37Rv_KO_Rv1272	0.568	1.143
H37Rv_KO_SugABC	0.301	0.842
H37Rv_KO_MbtN	0.92	0.76
Trans05	1.347	1.468
macrophage_unactivated	0.139	0.615
IL1	-0.792	-0.329
Rapamycin	-0.344	-0.307
Tcell	-0.15	-0.476
GMCSF	0.364	-0.869
IFNab	-0.369	-0.115
IFNg	0.024	0.139
IFNg_GMCSF1	-0.264	-0.478
Rv1432_day32	0.068	0.01
Rv1565c_day32	0.019	0.0
secA2_input	-0.753	0.114
delta_Rv3594	0.044	0.061
delta_Rv3717	-0.059	-0.609
delta_Rv3811	-0.123	0.0
delta_Rv0954	-0.69	-0.561
PonA1	-0.125	-0.38
EccD1_KO	0.158	0.51
EspI_KO	-0.08	0.853
PE35_KO	0.099	1.103
PPE68_KO	0.067	0.745
glycerol2	0.115	0.303
lignocerate	-0.438	0.247
oleate	0.644	0.251
phosphatidylcholine	0.409	0.356
acetate	-1.159	-0.318
glucAc	-1.522	-0.209
Rv0950ko	0.075	0.666
Rv1096ko	-0.995	-0.344
Rv3684ko	-0.305	0.131
delta_otsA_trehalose	-0.338	-0.462