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 Rv1918c/PPE35:

update plot	correlation	link to info on gene
Rv2735c/-	(cc=0.7314)	info on Rv2735c/-
Rv1521/fadD25	(cc=0.7076)	info on Rv1521/fadD25
Rv2519/PE26	(cc=0.7025)	info on Rv2519/PE26
Rv1984c/cfp21	(cc=0.7018)	info on Rv1984c/cfp21
Rv1059/-	(cc=0.6928)	info on Rv1059/-
Rv1548c/PPE21	(cc=0.6921)	info on Rv1548c/PPE21
Rv2430c/PPE41	(cc=0.6532)	info on Rv2430c/PPE41
Rv0469/umaA	(cc=0.6481)	info on Rv0469/umaA
Rv1504c/-	(cc=0.6464)	info on Rv1504c/-
Rv1616/-	(cc=0.644)	info on Rv1616/-

Correlation of Rv1918c/PPE35 with Rv2735c/-

Normalized LFCs for Rv1918c/PPE35:
(description and provenance of datasets)

	Rv1918c/PPE35	Rv2735c/-
Fe_supp_jason_reseq	0.426	0.731
low_pH_jason_reseq	-0.127	0.418
NO_jason_reseq	-0.326	0.249
B6_jason_reseq	-0.212	-0.614
MHCII_jason_reseq	-0.42	-0.111
Isoniazid02	0.439	-0.067
Rifampicin4	0.463	0.192
Ethambutol3	0.449	-0.068
Meropenem3	0.129	0.434
Vancomycin16	0.18	0.048
Rv2680_day32	-0.526	0.554
H37Rv_KO_MarP	-0.339	-0.341
hypoxia_3wks	0.06	0.315
hypoxia_6wks	-0.031	0.395
glycerol	-0.671	0.089
cholesterol	0.318	-0.343
AJ	0.432	0.671
Bibs02	0.189	0.631
Bibs02c	0.083	0.58
BL6	0.442	0.952
BL6a	0.641	1.522
BXD01	0.383	0.742
BXD010	0.525	1.552
BXD011	0.747	1.348
BXD03	0.904	1.483
BXD04	0.687	1.288
BXD05	0.8	1.268
BXD06	0.584	1.007
BXD07	0.666	1.504
BXD08	0.605	0.557
BXD09	0.602	1.226
CAST	0.21	0.586
CCcont	0.226	0.515
DS01	0.185	0.941
DS02	0.17	0.526
DS04	0.128	1.122
DS0c	0.058	0.335
GP01	0.102	1.8
GP02	0.421	1.821
GP0c	0.658	1.168
NOD	0.286	0.571
NZO	0.23	0.03
PWK	0.153	0.567
H37Rv_KO_CtpC	0.711	1.627
H37Rv_KO_CtpD	1.161	1.492
H37Rv_KO_Rv1272	1.414	1.96
H37Rv_KO_SugABC	0.711	0.664
H37Rv_KO_MbtN	1.033	1.849
Trans05	1.383	1.918
macrophage_unactivated	0.533	0.562
IL1	0.329	0.4
Rapamycin	0.411	0.107
Tcell	0.437	0.44
GMCSF	0.354	-0.259
IFNab	0.151	0.441
IFNg	0.166	0.214
IFNg_GMCSF1	0.738	0.591
Rv1432_day32	0.562	0.557
Rv1565c_day32	-0.227	0.257
secA2_input	-0.441	-0.379
delta_Rv3594	-0.106	1.195
delta_Rv3717	-0.257	0.39
delta_Rv3811	0.366	0.9
delta_Rv0954	0.014	0.236
PonA1	-0.22	0.426
EccD1_KO	-0.572	-0.526
EspI_KO	-0.365	-0.154
PE35_KO	-0.44	-0.525
PPE68_KO	-0.518	-0.48
glycerol2	-0.422	-0.359
lignocerate	-0.242	-0.233
oleate	-0.041	-0.098
phosphatidylcholine	-0.21	-0.08
acetate	-0.47	-0.214
glucAc	-0.123	-0.488
Rv0950ko	-0.488	0.528
Rv1096ko	-1.001	-0.48
Rv3684ko	-0.347	-0.147
delta_otsA_trehalose	-0.684	0.357