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sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
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supplemental table with gene and transcript expression stats results #93

Closed sr320 closed 9 months ago

sr320 commented 9 months ago

including different maximum number of transcripts expressed difference in predominant isoform etc,

kubu4 commented 9 months ago

How are you picturing the layout of this table?

Is this organized something like:

gene S13M_max_transcripts S13M_predominant_isoform
gene-01 3 XM_78543.2
sr320 commented 9 months ago

Within sex, for each gene there should be a max number of transcripts for control and for exposed.. same with predom isoform. Text might provide guidance... see below for female max number of transcripts (go head and create table of ALL genes even if they do not change.

A total of 3,966 genes were identified which had a different maximum number of transcripts expressed between female controls and female OA-exposed samples. Of those, the female controls had 2,437 (61.4%) genes with increases in the maximum number of transcripts, while the female OA-exposed samples had 1,529 (38.6%) genes with increases in the maximum number of transcripts.

kubu4 commented 9 months ago

Gotcha. Thanks.

kubu4 commented 9 months ago

Added table here:

https://raw.githubusercontent.com/sr320/ceabigr/main/supplemental-files/fmcoe-max-predom-isos.csv

This is what it looks like:

gene_name     control_females_max_transcript_counts  control_males_max_transcript_counts  exposed_females_max_transcript_counts  exposed_males_max_transcript_counts  max_transcript_counts  females_controls_predom_isoform  females_exposed_predom_isoform  males_controls_predom_isoform  males_exposed_predom_isoform
ATP6          1                                      1                                    1                                      1                                    1                      gene-ATP6                        gene-ATP6                       gene-ATP6                      gene-ATP6
COX1          1                                      1                                    1                                      1                                    1                      gene-COX1                        gene-COX1                       gene-COX1                      gene-COX1
COX2          1                                      1                                    1                                      1                                    1                      gene-COX2                        gene-COX2                       gene-COX2                      gene-COX2
COX3          1                                      1                                    1                                      1                                    1                      gene-COX3                        gene-COX3                       gene-COX3                      gene-COX3
CYTB          1                                      1                                    1                                      1                                    1                      gene-CYTB                        gene-CYTB                       gene-CYTB                      gene-CYTB
LOC111099029  1                                      1                                    1                                      1                                    1                      rna-XM_022458270.1               rna-XM_022458270.1              rna-XM_022458270.1             rna-XM_022458270.1
LOC111099030  1                                      1                                    1                                      1                                    1                      rna-XM_022430679.1               rna-XM_022430679.1              rna-XM_022430679.1             rna-XM_022430679.1
LOC111099031  1                                      1                                    0                                      1                                    1                      rna-XM_022430340.1               rna-XM_022430340.1              rna-XM_022430340.1             rna-XM_022430340.1
LOC111099032  1                                      1                                    1                                      1                                    1                      rna-XM_022430343.1               rna-XM_022430343.1              rna-XM_022430343.1             rna-XM_022430343.1

Is that what you had in mind?

sr320 commented 9 months ago

Is that what you had in mind?

yep looks great!

I think the other thing we are looking for on this is a table with expression values (fpkms?). genes and isoforms.

kubu4 commented 9 months ago

expression values (fpkms?). genes and isoforms

Mean FPKM per gene?

Mean FPKM for each isoform or just predominant isoform?

sr320 commented 9 months ago

what do you already have from workflow?

kubu4 commented 9 months ago

FPKM for each individual sample for each gene and each transcript.

sr320 commented 9 months ago

lets go with that then...

kubu4 commented 9 months ago

Okay. I actually went ahead an calculated means, too.

I'll just add it all in!

kubu4 commented 9 months ago

Updated table:

gene_name     females_controls_max_transcript_counts  males_controls_max_transcript_counts  females_exposed_max_transcript_counts  males_exposed_max_transcript_counts  max_transcript_counts  females_controls_predom_isoform  females_exposed_predom_isoform  males_controls_predom_isoform  males_exposed_predom_isoform  females_controls_predom_expression  females_exposed_predom_expression  males_controls_predom_expression  males_exposed_predom_expression  females_controls_mean_gene_FPKM  females_exposed_mean_gene_FPKM  males_controls_mean_gene_FPKM  males_exposed_mean_gene_FPKM
ATP6          1                                       1                                     1                                      1                                    1                      gene-ATP6                        gene-ATP6                       gene-ATP6                      gene-ATP6                     1556.936656                         1624.41369683333                   98.71285                          201.322307                       1487.778078375                   1631.140611375                  174.2921615                    164.043459666667
COX1          1                                       1                                     1                                      1                                    1                      gene-COX1                        gene-COX1                       gene-COX1                      gene-COX1                     2620.65207916667                    2420.26405716667                   159.495554                        537.79844075                     2580.701129125                   2463.376190625                  360.12567675                   412.768308833333
COX2          1                                       1                                     1                                      1                                    1                      gene-COX2                        gene-COX2                       gene-COX2                      gene-COX2                     3303.03234183333                    3077.3059535                       177.196696                        674.34632525                     3332.35374                       3219.08598925                   426.6481855                    498.821871333333
COX3          1                                       1                                     1                                      1                                    1                      gene-COX3                        gene-COX3                       gene-COX3                      gene-COX3                     1337.4900205                        1280.654135                        154.0915025                       398.70069325                     1276.953951625                   1332.629574625                  318.658322                     316.4707085
CYTB          1                                       1                                     1                                      1                                    1                      gene-CYTB                        gene-CYTB                       gene-CYTB                      gene-CYTB                     3732.32512833333                    3929.06415383333                   218.464097                        836.67610975                     3605.66468875                    3944.190358625                  509.55340325                   615.221576666667
LOC111099029  1                                       1                                     1                                      1                                    1                      rna-XM_022458270.1               rna-XM_022458270.1              rna-XM_022458270.1             rna-XM_022458270.1            6.09067216666667                    12.9312403333333                   2.4887975                         3.320988                         5.245312375                      11.006785375                    2.86018675                     2.622809
LOC111099030  1                                       1                                     1                                      1                                    1                      rna-XM_022430679.1               rna-XM_022430679.1              rna-XM_022430679.1             rna-XM_022430679.1            0.222926833333333                   0.2309585                          8.1297515                         6.36821525                       0.463488875                      0.27486975                      6.958755                       7.22927866666667
LOC111099031  1                                       1                                     0                                      1                                    1                      rna-XM_022430340.1               rna-XM_022430340.1              rna-XM_022430340.1             rna-XM_022430340.1            0.0442751666666667                  0                                  3.5993885                         2.307631                         0.050484                         0                               2.8397895                      2.649375
LOC111099032  1                                       1                                     1                                      1                                    1                      rna-XM_022430343.1               rna-XM_022430343.1              rna-XM_022430343.1             rna-XM_022430343.1            0.305045333333333                   0.310936166666667                  13.075051                         10.35354275                      0.24102725                       0.38273075                      10.35293625                    12.3677855