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 Rv3225c/-:

update plot	correlation	link to info on gene
Rv2601/speE	(cc=0.4966)	info on Rv2601/speE
Rv2646/-	(cc=0.491)	info on Rv2646/-
Rv3093c/-	(cc=0.4804)	info on Rv3093c/-
Rv2917/-	(cc=0.4803)	info on Rv2917/-
Rv2125/-	(cc=0.4799)	info on Rv2125/-
Rv2765/-	(cc=0.47)	info on Rv2765/-
Rv0597c/-	(cc=0.4647)	info on Rv0597c/-
Rv3401/-	(cc=0.4445)	info on Rv3401/-
Rv1982c/vapC36	(cc=0.4366)	info on Rv1982c/vapC36
Rv0132c/fgd2	(cc=0.4358)	info on Rv0132c/fgd2

Correlation of Rv3225c/- with Rv3401/-

Normalized LFCs for Rv3225c/-:
(description and provenance of datasets)

	Rv3225c/-	Rv3401/-
Fe_supp_jason_reseq	0.046	0.0
low_pH_jason_reseq	-0.711	-0.659
NO_jason_reseq	0.173	-0.026
B6_jason_reseq	0.134	0.695
MHCII_jason_reseq	0.415	0.952
Isoniazid02	0.271	0.383
Rifampicin4	-0.826	0.244
Ethambutol3	0.134	0.72
Meropenem3	0.098	1.518
Vancomycin16	-0.021	-0.082
Rv2680_day32	0.258	1.336
H37Rv_KO_MarP	0.339	0.23
hypoxia_3wks	-0.215	-0.068
hypoxia_6wks	0.192	-0.035
glycerol	-0.392	-0.053
cholesterol	0.057	1.523
AJ	-0.027	-0.131
Bibs02	0.072	0.567
Bibs02c	0.461	-0.156
BL6	0.21	-0.906
BL6a	-0.265	-0.97
BXD01	-0.73	-0.89
BXD010	-0.61	-0.854
BXD011	-0.859	-0.556
BXD03	-0.733	-0.564
BXD04	-0.556	-0.606
BXD05	-0.729	-0.793
BXD06	-0.384	-1.097
BXD07	-0.064	-0.687
BXD08	-0.598	-0.624
BXD09	-0.583	-0.892
CAST	0.038	0.269
CCcont	-0.229	-1.095
DS01	-0.014	0.548
DS02	-0.181	0.421
DS04	0.87	0.602
DS0c	0.247	0.404
GP01	1.094	0.349
GP02	0.869	0.307
GP0c	-0.038	-0.109
NOD	1.023	0.906
NZO	-0.241	-0.205
PWK	0.141	-0.354
H37Rv_KO_CtpC	0.258	-0.54
H37Rv_KO_CtpD	-0.237	0.537
H37Rv_KO_Rv1272	-0.481	-0.305
H37Rv_KO_SugABC	0.623	-0.478
H37Rv_KO_MbtN	-0.118	-0.036
Trans05	-0.254	0.384
macrophage_unactivated	-0.167	-0.925
IL1	-0.222	-0.97
Rapamycin	0.338	-0.829
Tcell	-0.499	-0.671
GMCSF	0.026	-0.57
IFNab	-0.16	-1.022
IFNg	-0.171	-0.123
IFNg_GMCSF1	0.286	0.251
Rv1432_day32	0.102	0.757
Rv1565c_day32	-0.014	0.763
secA2_input	-0.114	0.261
delta_Rv3594	-0.211	-0.223
delta_Rv3717	0.063	-0.227
delta_Rv3811	-0.015	-0.235
delta_Rv0954	-0.39	0.088
PonA1	0.624	0.323
EccD1_KO	0.253	-0.033
EspI_KO	-0.482	-0.086
PE35_KO	-0.117	-0.146
PPE68_KO	-0.163	-0.16
glycerol2	-0.856	0.083
lignocerate	-0.358	-0.571
oleate	-0.54	-0.647
phosphatidylcholine	-0.549	-0.13
acetate	-0.929	-0.191
glucAc	-0.294	-0.389
Rv0950ko	0.238	0.093
Rv1096ko	0.172	0.184
Rv3684ko	-0.154	-0.105
delta_otsA_trehalose	-0.467	0.465