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 Rv1560/vapB11:

update plot	correlation	link to info on gene
Rv0371c/-	(cc=0.6612)	info on Rv0371c/-
Rv3152/nuoH	(cc=0.5913)	info on Rv3152/nuoH
Rv3218/-	(cc=0.5641)	info on Rv3218/-
Rv3567c/hsaB	(cc=0.545)	info on Rv3567c/hsaB
Rv3143/-	(cc=0.5405)	info on Rv3143/-
Rv2430c/PPE41	(cc=0.5295)	info on Rv2430c/PPE41
Rv0930/pstA1	(cc=0.5255)	info on Rv0930/pstA1
Rv1278/-	(cc=0.5223)	info on Rv1278/-
Rv0822c/-	(cc=0.5175)	info on Rv0822c/-
Rv1891/-	(cc=0.5081)	info on Rv1891/-

Correlation of Rv1560/vapB11 with Rv1278/-

Normalized LFCs for Rv1560/vapB11:
(description and provenance of datasets)

	Rv1560/vapB11	Rv1278/-
Fe_supp_jason_reseq	-2.395	0.74
low_pH_jason_reseq	-0.151	0.873
NO_jason_reseq	0.591	-0.302
B6_jason_reseq	-2.447	-0.128
MHCII_jason_reseq	-1.809	-0.684
Isoniazid02	0.141	-0.969
Rifampicin4	1.17	0.517
Ethambutol3	0.333	-0.871
Meropenem3	0.488	-0.858
Vancomycin16	0.499	-0.44
Rv2680_day32	-1.282	-1.288
H37Rv_KO_MarP	-0.567	-0.563
hypoxia_3wks	-1.978	-0.471
hypoxia_6wks	-0.217	0.334
glycerol	-0.157	1.562
cholesterol	-0.509	0.268
AJ	0.471	0.956
Bibs02	-0.642	-0.489
Bibs02c	3.812	0.202
BL6	4.189	1.137
BL6a	3.734	0.905
BXD01	2.879	0.944
BXD010	2.52	0.791
BXD011	3.56	0.554
BXD03	2.371	0.861
BXD04	1.221	1.577
BXD05	4.371	1.166
BXD06	2.466	0.897
BXD07	2.957	0.956
BXD08	1.622	1.029
BXD09	3.392	0.97
CAST	-0.179	0.15
CCcont	2.533	0.951
DS01	0.479	0.974
DS02	1.493	0.744
DS04	0.62	0.413
DS0c	3.804	0.894
GP01	1.109	1.786
GP02	2.859	0.603
GP0c	4.362	1.338
NOD	-0.174	-0.156
NZO	2.852	0.682
PWK	-0.315	0.065
H37Rv_KO_CtpC	-0.261	0.973
H37Rv_KO_CtpD	-0.445	-0.088
H37Rv_KO_Rv1272	2.605	1.179
H37Rv_KO_SugABC	-0.159	0.408
H37Rv_KO_MbtN	-0.26	1.345
Trans05	1.171	0.832
macrophage_unactivated	0.189	-0.256
IL1	0.11	-0.24
Rapamycin	0.568	-0.163
Tcell	0.567	0.0
GMCSF	1.402	0.694
IFNab	0.877	0.305
IFNg	0.984	-0.775
IFNg_GMCSF1	0.336	-0.525
Rv1432_day32	0.0	0.083
Rv1565c_day32	0.0	-0.087
secA2_input	1.191	0.0
delta_Rv3594	-0.696	0.04
delta_Rv3717	0.583	0.736
delta_Rv3811	-2.602	0.509
delta_Rv0954	-1.243	0.066
PonA1	1.973	0.115
EccD1_KO	0.0	-1.059
EspI_KO	-1.452	-1.092
PE35_KO	1.963	0.271
PPE68_KO	0.902	0.442
glycerol2	-0.708	-0.883
lignocerate	-1.299	-0.262
oleate	-2.657	-0.417
phosphatidylcholine	-0.297	-0.612
acetate	-0.17	0.143
glucAc	0.033	0.328
Rv0950ko	0.941	0.0
Rv1096ko	0.941	1.077
Rv3684ko	-1.307	0.164
delta_otsA_trehalose	0.0	0.798