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 Rv3007c/-:

update plot	correlation	link to info on gene
Rv0064A/vapB1	(cc=0.4545)	info on Rv0064A/vapB1
Rv0456c/echA2	(cc=0.4446)	info on Rv0456c/echA2
Rv1515c/-	(cc=0.419)	info on Rv1515c/-
Rv2804c/-	(cc=0.4133)	info on Rv2804c/-
Rv3215/entC	(cc=0.4128)	info on Rv3215/entC
Rv1730c/-	(cc=0.3998)	info on Rv1730c/-
Rv3917c/parB	(cc=0.3921)	info on Rv3917c/parB
Rv1465/-	(cc=0.3915)	info on Rv1465/-
Rv2454c/-	(cc=0.387)	info on Rv2454c/-
Rv3729/-	(cc=0.3846)	info on Rv3729/-

Correlation of Rv3007c/- with Rv0456c/echA2

Normalized LFCs for Rv3007c/-:
(description and provenance of datasets)

	Rv3007c/-	Rv0456c/echA2
Fe_supp_jason_reseq	-0.69	-0.047
low_pH_jason_reseq	0.136	-0.427
NO_jason_reseq	-0.168	-0.764
B6_jason_reseq	0.09	0.514
MHCII_jason_reseq	0.131	0.323
Isoniazid02	-0.194	-0.349
Rifampicin4	-0.114	-0.057
Ethambutol3	0.203	-0.103
Meropenem3	0.2	-0.268
Vancomycin16	0.199	0.215
Rv2680_day32	0.922	0.328
H37Rv_KO_MarP	0.691	-0.212
hypoxia_3wks	0.267	-0.096
hypoxia_6wks	0.113	-0.566
glycerol	0.778	0.92
cholesterol	0.484	0.064
AJ	0.619	0.556
Bibs02	0.699	-0.388
Bibs02c	0.153	0.615
BL6	-0.19	-0.422
BL6a	0.034	0.099
BXD01	-0.018	0.244
BXD010	-0.478	-0.614
BXD011	0.532	-0.111
BXD03	-0.408	0.018
BXD04	0.008	-0.532
BXD05	0.705	-0.318
BXD06	0.19	0.199
BXD07	-0.019	0.4
BXD08	0.208	-0.414
BXD09	0.152	-0.344
CAST	0.596	0.839
CCcont	-0.048	-0.089
DS01	-0.169	-0.358
DS02	-0.091	0.276
DS04	0.35	0.364
DS0c	0.228	0.041
GP01	-0.031	-1.084
GP02	0.254	1.232
GP0c	0.087	-1.168
NOD	0.939	0.015
NZO	0.853	1.165
PWK	0.811	1.653
H37Rv_KO_CtpC	1.414	1.001
H37Rv_KO_CtpD	0.125	-0.545
H37Rv_KO_Rv1272	0.225	-0.452
H37Rv_KO_SugABC	0.73	-0.334
H37Rv_KO_MbtN	-0.648	-0.164
Trans05	-0.013	-0.55
macrophage_unactivated	0.044	0.732
IL1	0.436	-0.62
Rapamycin	-0.117	-0.328
Tcell	0.381	0.218
GMCSF	0.251	-0.38
IFNab	0.193	-0.033
IFNg	0.291	-0.353
IFNg_GMCSF1	-0.016	-0.87
Rv1432_day32	0.424	0.535
Rv1565c_day32	0.033	1.256
secA2_input	-1.124	0.091
delta_Rv3594	-0.021	0.878
delta_Rv3717	-0.082	-0.175
delta_Rv3811	0.062	0.177
delta_Rv0954	0.214	-0.088
PonA1	0.772	-0.511
EccD1_KO	0.424	0.599
EspI_KO	0.69	0.459
PE35_KO	0.111	0.49
PPE68_KO	0.141	0.515
glycerol2	0.895	0.474
lignocerate	1.022	0.106
oleate	0.499	0.152
phosphatidylcholine	0.868	0.331
acetate	0.115	0.199
glucAc	0.128	-0.42
Rv0950ko	-0.555	-1.423
Rv1096ko	-0.745	-1.472
Rv3684ko	-0.927	-1.235
delta_otsA_trehalose	0.123	0.774