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 Rv0074/-:

update plot	correlation	link to info on gene
Rv0305c/PPE6	(cc=0.4881)	info on Rv0305c/PPE6
Rv0907/-	(cc=0.4872)	info on Rv0907/-
Rv1585c/-	(cc=0.4725)	info on Rv1585c/-
Rv0255c/cobQ1	(cc=0.4664)	info on Rv0255c/cobQ1
Rv0112/gca	(cc=0.4539)	info on Rv0112/gca
Rv3787c/-	(cc=0.4534)	info on Rv3787c/-
Rv3857c/-	(cc=0.452)	info on Rv3857c/-
Rv0822c/-	(cc=0.4427)	info on Rv0822c/-
Rv2430c/PPE41	(cc=0.4233)	info on Rv2430c/PPE41
Rv1664/pks9	(cc=0.423)	info on Rv1664/pks9

Correlation of Rv0074/- with Rv0822c/-

Normalized LFCs for Rv0074/-:
(description and provenance of datasets)

	Rv0074/-	Rv0822c/-
Fe_supp_jason_reseq	-0.65	-0.336
low_pH_jason_reseq	-0.172	-0.756
NO_jason_reseq	-0.105	-0.27
B6_jason_reseq	-0.694	-1.076
MHCII_jason_reseq	-0.122	-0.457
Isoniazid02	-0.049	0.109
Rifampicin4	0.208	-0.19
Ethambutol3	0.081	0.764
Meropenem3	0.193	0.317
Vancomycin16	0.374	0.334
Rv2680_day32	0.247	-0.501
H37Rv_KO_MarP	0.329	-0.617
hypoxia_3wks	0.391	0.159
hypoxia_6wks	0.09	0.157
glycerol	-0.799	-0.161
cholesterol	-0.351	0.331
AJ	-0.067	0.353
Bibs02	-1.113	0.144
Bibs02c	0.02	0.502
BL6	-0.761	0.743
BL6a	-0.019	1.042
BXD01	-0.212	0.715
BXD010	-0.1	1.18
BXD011	-0.152	0.663
BXD03	0.276	1.16
BXD04	0.012	0.707
BXD05	0.487	0.905
BXD06	-0.174	1.181
BXD07	-0.32	1.02
BXD08	0.609	0.768
BXD09	-0.276	1.011
CAST	-0.204	0.536
CCcont	-0.551	0.625
DS01	0.743	0.549
DS02	0.041	0.181
DS04	0.663	0.869
DS0c	0.288	0.528
GP01	0.036	1.013
GP02	0.737	0.996
GP0c	0.246	0.214
NOD	1.417	0.83
NZO	-0.709	0.763
PWK	-0.153	1.06
H37Rv_KO_CtpC	0.578	0.627
H37Rv_KO_CtpD	0.125	1.105
H37Rv_KO_Rv1272	0.311	0.322
H37Rv_KO_SugABC	1.183	0.431
H37Rv_KO_MbtN	-0.01	0.005
Trans05	1.075	0.975
macrophage_unactivated	0.051	0.59
IL1	-0.243	0.139
Rapamycin	-0.147	0.261
Tcell	0.629	0.678
GMCSF	0.473	0.961
IFNab	-0.508	0.532
IFNg	0.043	0.326
IFNg_GMCSF1	0.383	0.16
Rv1432_day32	-0.485	0.681
Rv1565c_day32	-0.885	-1.72
secA2_input	-0.291	-0.517
delta_Rv3594	-0.534	-0.116
delta_Rv3717	-1.155	-0.316
delta_Rv3811	-1.038	-0.29
delta_Rv0954	-0.267	-0.649
PonA1	0.695	-0.352
EccD1_KO	-0.46	-0.5
EspI_KO	-1.132	-0.117
PE35_KO	-0.525	-0.23
PPE68_KO	-0.739	-0.784
glycerol2	-0.161	-0.175
lignocerate	-0.532	-0.524
oleate	0.047	0.007
phosphatidylcholine	-0.531	-0.62
acetate	-0.379	-1.034
glucAc	-0.549	-0.789
Rv0950ko	-0.467	-0.335
Rv1096ko	0.259	0.44
Rv3684ko	-0.098	0.013
delta_otsA_trehalose	1.473	0.707