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 Rv3224/-:

update plot	correlation	link to info on gene
Rv0454/-	(cc=0.5311)	info on Rv0454/-
Rv0644c/mmaA2	(cc=0.528)	info on Rv0644c/mmaA2
Rv0048c/-	(cc=0.5093)	info on Rv0048c/-
Rv3158/nuoN	(cc=0.5076)	info on Rv3158/nuoN
Rv3429/PPE59	(cc=0.5051)	info on Rv3429/PPE59
Rv1520/-	(cc=0.4988)	info on Rv1520/-
Rv2107/PE22	(cc=0.4955)	info on Rv2107/PE22
Rv3842c/glpQ1	(cc=0.4854)	info on Rv3842c/glpQ1
Rv1866/-	(cc=0.4848)	info on Rv1866/-
Rv1550/fadD11	(cc=0.4841)	info on Rv1550/fadD11

Correlation of Rv3224/- with Rv0644c/mmaA2

Normalized LFCs for Rv3224/-:
(description and provenance of datasets)

	Rv3224/-	Rv0644c/mmaA2
Fe_supp_jason_reseq	-0.543	-0.227
low_pH_jason_reseq	-0.482	1.2
NO_jason_reseq	-0.402	0.882
B6_jason_reseq	0.656	0.5
MHCII_jason_reseq	0.222	-0.154
Isoniazid02	0.365	0.963
Rifampicin4	-0.116	-0.46
Ethambutol3	1.892	2.038
Meropenem3	0.788	0.24
Vancomycin16	0.048	1.926
Rv2680_day32	0.111	3.409
H37Rv_KO_MarP	-0.175	0.831
hypoxia_3wks	0.183	3.688
hypoxia_6wks	0.426	4.063
glycerol	-0.933	-0.208
cholesterol	-0.451	-0.986
AJ	-0.145	0.427
Bibs02	-0.253	-0.621
Bibs02c	0.177	-0.918
BL6	0.468	2.082
BL6a	0.26	2.393
BXD01	0.571	3.306
BXD010	0.657	2.737
BXD011	0.51	3.421
BXD03	0.196	1.467
BXD04	0.529	1.779
BXD05	0.464	2.071
BXD06	0.582	2.375
BXD07	0.655	2.536
BXD08	0.661	2.516
BXD09	0.443	3.211
CAST	0.409	0.611
CCcont	-0.314	0.434
DS01	0.08	-1.353
DS02	0.438	0.203
DS04	0.194	1.025
DS0c	-0.357	-0.332
GP01	1.121	2.536
GP02	0.168	2.939
GP0c	0.217	1.688
NOD	0.132	1.593
NZO	0.051	1.231
PWK	-0.202	-0.347
H37Rv_KO_CtpC	0.261	0.238
H37Rv_KO_CtpD	0.824	1.411
H37Rv_KO_Rv1272	0.231	2.077
H37Rv_KO_SugABC	0.992	1.754
H37Rv_KO_MbtN	0.594	2.539
Trans05	0.5	2.578
macrophage_unactivated	-0.496	-1.171
IL1	-0.205	-0.326
Rapamycin	-0.402	-1.252
Tcell	-0.134	1.665
GMCSF	-0.193	-0.914
IFNab	-0.124	-1.778
IFNg	-0.679	-1.547
IFNg_GMCSF1	-0.399	-1.574
Rv1432_day32	0.679	5.684
Rv1565c_day32	-0.259	0.229
secA2_input	-0.091	-0.753
delta_Rv3594	0.239	0.817
delta_Rv3717	0.539	2.513
delta_Rv3811	0.571	1.089
delta_Rv0954	-0.443	-0.756
PonA1	-0.11	-1.215
EccD1_KO	-0.02	-1.681
EspI_KO	0.588	-1.646
PE35_KO	0.277	-1.555
PPE68_KO	0.378	-2.332
glycerol2	0.199	1.843
lignocerate	0.33	1.074
oleate	0.617	0.81
phosphatidylcholine	0.192	1.455
acetate	-0.043	0.188
glucAc	-0.299	0.068
Rv0950ko	-0.145	-0.178
Rv1096ko	-0.13	-1.246
Rv3684ko	0.272	0.2
delta_otsA_trehalose	0.139	-1.578