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 Rv1302/rfe:

update plot	correlation	link to info on gene
Rv0110/-	(cc=0.4599)	info on Rv0110/-
Rv0877/-	(cc=0.4526)	info on Rv0877/-
Rv0047c/-	(cc=0.444)	info on Rv0047c/-
Rv0158/-	(cc=0.4328)	info on Rv0158/-
Rv2957/-	(cc=0.4311)	info on Rv2957/-
Rv0182c/sigG	(cc=0.4139)	info on Rv0182c/sigG
Rv1072/-	(cc=0.407)	info on Rv1072/-
Rv2617c/-	(cc=0.4012)	info on Rv2617c/-
Rv3853/rraA	(cc=0.3996)	info on Rv3853/rraA
Rv2079/-	(cc=0.3978)	info on Rv2079/-

Correlation of Rv1302/rfe with Rv2957/-

Normalized LFCs for Rv1302/rfe:
(description and provenance of datasets)

	Rv1302/rfe	Rv2957/-
Fe_supp_jason_reseq	1.437	0.507
low_pH_jason_reseq	0.465	-0.46
NO_jason_reseq	1.173	-0.018
B6_jason_reseq	0.957	0.052
MHCII_jason_reseq	-0.309	0.319
Isoniazid02	0.453	-0.784
Rifampicin4	-0.192	0.417
Ethambutol3	0.732	0.316
Meropenem3	0.502	-0.769
Vancomycin16	0.18	-0.17
Rv2680_day32	1.779	0.675
H37Rv_KO_MarP	-0.766	0.492
hypoxia_3wks	-0.14	-0.12
hypoxia_6wks	-0.146	-0.236
glycerol	-0.054	-0.018
cholesterol	-1.01	-0.17
AJ	0.674	0.171
Bibs02	-0.968	-0.04
Bibs02c	-0.268	0.399
BL6	-1.086	0.256
BL6a	0.154	0.131
BXD01	0.737	0.434
BXD010	0.115	0.519
BXD011	0.931	0.322
BXD03	-0.444	0.536
BXD04	0.228	0.994
BXD05	0.201	0.11
BXD06	0.786	0.465
BXD07	0.285	0.422
BXD08	1.099	0.268
BXD09	0.88	0.49
CAST	1.525	0.347
CCcont	-0.791	0.191
DS01	-0.527	-0.123
DS02	-0.09	0.221
DS04	-0.672	-0.228
DS0c	-0.671	0.358
GP01	1.155	0.782
GP02	0.603	0.576
GP0c	0.907	0.039
NOD	0.952	0.692
NZO	0.053	-0.402
PWK	0.026	0.395
H37Rv_KO_CtpC	1.292	0.936
H37Rv_KO_CtpD	1.526	0.909
H37Rv_KO_Rv1272	0.598	1.143
H37Rv_KO_SugABC	0.171	0.842
H37Rv_KO_MbtN	1.816	0.76
Trans05	0.611	1.468
macrophage_unactivated	-0.069	0.615
IL1	-0.332	-0.329
Rapamycin	-1.295	-0.307
Tcell	0.404	-0.476
GMCSF	-0.615	-0.869
IFNab	-0.704	-0.115
IFNg	0.168	0.139
IFNg_GMCSF1	-0.654	-0.478
Rv1432_day32	0.305	0.01
Rv1565c_day32	-0.294	0.0
secA2_input	1.169	0.114
delta_Rv3594	-0.369	0.061
delta_Rv3717	-0.5	-0.609
delta_Rv3811	-0.407	0.0
delta_Rv0954	-0.934	-0.561
PonA1	-0.082	-0.38
EccD1_KO	-0.082	0.51
EspI_KO	0.761	0.853
PE35_KO	0.07	1.103
PPE68_KO	0.586	0.745
glycerol2	0.838	0.303
lignocerate	0.175	0.247
oleate	1.191	0.251
phosphatidylcholine	0.957	0.356
acetate	-0.032	-0.318
glucAc	-0.039	-0.209
Rv0950ko	1.185	0.666
Rv1096ko	0.492	-0.344
Rv3684ko	1.844	0.131
delta_otsA_trehalose	-0.662	-0.462