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 Rv1091/PE_PGRS22:

update plot	correlation	link to info on gene
Rv0578c/PE_PGRS7	(cc=0.7327)	info on Rv0578c/PE_PGRS7
Rv0833/PE_PGRS13	(cc=0.714)	info on Rv0833/PE_PGRS13
Rv3512/PE_PGRS56	(cc=0.6852)	info on Rv3512/PE_PGRS56
Rv3345c/PE_PGRS50	(cc=0.6672)	info on Rv3345c/PE_PGRS50
Rv1087/PE_PGRS21	(cc=0.6475)	info on Rv1087/PE_PGRS21
Rv3514/PE_PGRS57	(cc=0.6168)	info on Rv3514/PE_PGRS57
Rv3508/PE_PGRS54	(cc=0.6047)	info on Rv3508/PE_PGRS54
Rv2479c/-	(cc=0.6031)	info on Rv2479c/-
Rv3355c/-	(cc=0.6029)	info on Rv3355c/-
Rv3380c/-	(cc=0.6001)	info on Rv3380c/-

Correlation of Rv1091/PE_PGRS22 with Rv3380c/-

Normalized LFCs for Rv1091/PE_PGRS22:
(description and provenance of datasets)

	Rv1091/PE_PGRS22	Rv3380c/-
Fe_supp_jason_reseq	-0.612	-0.158
low_pH_jason_reseq	-0.318	-0.361
NO_jason_reseq	-0.087	0.331
B6_jason_reseq	-0.686	-0.24
MHCII_jason_reseq	0.273	-0.083
Isoniazid02	-1.317	0.029
Rifampicin4	0.563	1.218
Ethambutol3	0.074	1.379
Meropenem3	0.268	-0.204
Vancomycin16	-0.348	0.138
Rv2680_day32	-0.091	0.095
H37Rv_KO_MarP	-0.202	-0.032
hypoxia_3wks	0.171	0.586
hypoxia_6wks	0.177	0.033
glycerol	1.072	-0.777
cholesterol	0.81	0.103
AJ	0.919	1.419
Bibs02	1.439	1.146
Bibs02c	0.985	1.625
BL6	-1.01	0.166
BL6a	0.531	0.931
BXD01	0.349	0.64
BXD010	0.155	0.872
BXD011	0.277	0.754
BXD03	0.043	0.688
BXD04	0.058	0.484
BXD05	0.473	0.975
BXD06	-0.258	0.454
BXD07	0.422	0.737
BXD08	0.103	0.489
BXD09	-0.046	0.634
CAST	0.247	1.341
CCcont	-0.609	0.168
DS01	0.45	0.83
DS02	0.688	0.791
DS04	0.568	1.136
DS0c	0.035	0.971
GP01	0.505	1.261
GP02	0.547	1.424
GP0c	0.472	0.851
NOD	0.488	1.588
NZO	-0.133	1.076
PWK	0.666	1.248
H37Rv_KO_CtpC	0.076	0.733
H37Rv_KO_CtpD	0.865	0.806
H37Rv_KO_Rv1272	2.015	0.626
H37Rv_KO_SugABC	-0.529	0.834
H37Rv_KO_MbtN	-0.667	0.52
Trans05	0.35	0.986
macrophage_unactivated	-0.527	-0.966
IL1	-1.883	-1.014
Rapamycin	-1.676	-1.074
Tcell	-1.245	-1.639
GMCSF	-0.747	-0.312
IFNab	-2.515	-1.37
IFNg	-1.307	-0.612
IFNg_GMCSF1	-0.669	-0.493
Rv1432_day32	0.441	0.533
Rv1565c_day32	-0.924	0.201
secA2_input	-0.211	0.128
delta_Rv3594	0.229	-0.197
delta_Rv3717	0.294	-0.185
delta_Rv3811	-0.168	-0.259
delta_Rv0954	-1.098	0.474
PonA1	0.21	-0.17
EccD1_KO	0.513	0.0
EspI_KO	-0.459	1.218
PE35_KO	0.067	0.718
PPE68_KO	0.074	0.294
glycerol2	-0.666	-0.556
lignocerate	-1.094	-0.375
oleate	-0.102	-1.049
phosphatidylcholine	-0.564	-0.643
acetate	-0.557	0.161
glucAc	-0.543	0.276
Rv0950ko	0.476	0.292
Rv1096ko	1.215	0.084
Rv3684ko	0.19	-0.118
delta_otsA_trehalose	0.272	0.38