Expression Plasticity

Coefficient of Variation Matrices

Summary of Available Data

The coefficient of variation (CV) of exon expression per gene provides a measure of expression plasticity. Higher CV values indicate greater variability in exon usage across samples, which may reflect alternative splicing or differential exon utilization under varying conditions.

Gene/Exon Counts by Data Type
Species Exon CV Genes Exon Count Features
Acropora pulchra 10,006 209,537
Porites evermanni 12,174 235,943
Pocillopora tuahiniensis 11,342 208,535

About the Data

The coefficient of variation (CV) matrix represents the variability of exon expression within each gene across samples. For each gene, the CV is calculated as the standard deviation of exon-level expression divided by the mean, providing a normalized measure of expression variability. This metric captures expression plasticity at the exon level, which may reflect:

  • Alternative splicing events: Genes with high CV may utilize different exons under different conditions
  • Differential exon usage: Environmental or developmental changes may shift which exons are predominantly expressed
  • Regulatory complexity: Higher CV values may indicate more complex post-transcriptional regulation

Genes with consistently low CV values show stable exon usage patterns, while those with high CV demonstrate greater plasticity in their transcript isoform composition.

The exon count matrix provides raw expression counts at the exon level for each gene across all samples. This data enables:

  • Differential exon usage analysis: Compare exon expression patterns between conditions or time points
  • Alternative splicing detection: Identify genes with variable exon inclusion/exclusion patterns
  • Isoform-level expression: Understand transcript diversity within genes
  • Foundation for CV calculation: The exon counts serve as the basis for computing the coefficient of variation metrics

Each row represents a unique exon-gene combination, with columns containing sample-specific read counts. This granular data supports detailed investigation of post-transcriptional regulation mechanisms.

Acropora pulchra

Exon CV

Download Exon CV

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries-molecular-calcification/M-multi-species/output/42-sample-exon-count/apul-cv_matrix.tsv 

Apul_exon_cv (first 4 rows)

gene_id ACR-139-TP1 ACR-139-TP2 ACR-139-TP3 ACR-139-TP4 ACR-145-TP1 ACR-145-TP2 ACR-145-TP3 ACR-145-TP4 ACR-150-TP1 ACR-150-TP2 ACR-150-TP3 ACR-150-TP4 ACR-173-TP1 ACR-173-TP2 ACR-173-TP3 ACR-173-TP4 ACR-186-TP1 ACR-186-TP2 ACR-186-TP3 ACR-186-TP4 ACR-225-TP1 ACR-225-TP2 ACR-225-TP3 ACR-225-TP4 ACR-229-TP1 ACR-229-TP2 ACR-229-TP3 ACR-229-TP4 ACR-237-TP1 ACR-237-TP2 ACR-237-TP3 ACR-237-TP4 ACR-244-TP1 ACR-244-TP2 ACR-244-TP3 ACR-244-TP4 ACR-265-TP1 ACR-265-TP2 ACR-265-TP3 ACR-265-TP4
FUN_000002 1.253149 1.459295 1.559335 1.501586 1.690242 1.561706 2.153062 1.8095480 1.603140 1.526080 1.561669 1.6144909 1.334518 1.4792108 1.8386216 1.8980180 1.670957 1.601578 1.907846 1.607626 2.171387 1.642301 1.6804043 2.098880 1.6461399 1.6087989 1.6154904 1.655420 1.8762816 1.5744080 1.6094628 1.759210 2.184346 1.4456277 1.580409 2.233075 2.114560 1.5391335 1.607415 1.895613
FUN_000005 1.364166 1.418916 1.634594 1.518412 1.799408 1.652290 2.150598 1.8900941 1.563371 1.554354 1.685137 1.6186851 1.499007 1.4931012 1.9026906 1.9478704 1.735855 1.631352 2.158144 1.666442 2.021534 1.451915 1.5568422 1.992537 1.8062502 1.6430678 1.6921592 1.721603 1.7649171 1.5733031 1.5980004 1.575181 2.395592 1.3619640 1.448016 2.352075 2.281185 1.6267156 1.655660 2.036010
FUN_000006 2.100386 2.667627 2.450932 2.375147 1.652450 2.118939 2.101496 2.1259688 1.739710 1.819126 2.054189 3.0402197 1.747776 1.8676316 2.8462572 1.8212509 2.151260 2.557701 2.458757 2.063010 2.024046 2.247349 1.9414914 2.028645 2.6606028 2.6490107 1.9779386 2.677791 3.0456633 1.8173096 1.7752594 3.158759 3.127497 2.1618006 2.174794 2.922029 2.285360 1.5691375 1.711227 2.424016
FUN_000009 2.368079 1.621147 2.542691 2.594972 1.049064 1.313179 1.109247 0.9176943 2.629302 1.290731 1.110591 0.6511769 1.069634 0.8050166 0.7207455 0.9679521 3.288474 2.532419 3.061590 2.638272 1.321873 2.089061 0.7210482 1.669759 0.6665453 0.5551272 0.7052224 2.179525 0.9262514 0.6716475 0.5434841 1.131846 1.439875 0.9460971 1.577500 2.175344 1.389332 0.7378416 2.257088 1.513227

Exon Count Matrix

Download Exon Count Matrix

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries-molecular-calcification/M-multi-species/output/40-exon-count-matrix/apul-exon_gene_count_matrix.csv 

Apul_exon_count (first 4 rows)

gene_id e_id chr strand start end ACR-139-TP1 ACR-139-TP2 ACR-139-TP3 ACR-139-TP4 ACR-145-TP1 ACR-145-TP2 ACR-145-TP3 ACR-145-TP4 ACR-150-TP1 ACR-150-TP2 ACR-150-TP3 ACR-150-TP4 ACR-173-TP1 ACR-173-TP2 ACR-173-TP3 ACR-173-TP4 ACR-186-TP1 ACR-186-TP2 ACR-186-TP3 ACR-186-TP4 ACR-225-TP1 ACR-225-TP2 ACR-225-TP3 ACR-225-TP4 ACR-229-TP1 ACR-229-TP2 ACR-229-TP3 ACR-229-TP4 ACR-237-TP1 ACR-237-TP2 ACR-237-TP3 ACR-237-TP4 ACR-244-TP1 ACR-244-TP2 ACR-244-TP3 ACR-244-TP4 ACR-265-TP1 ACR-265-TP2 ACR-265-TP3 ACR-265-TP4
FUN_000001 1 ntLink_0 + 1105 1188 57 0 0 42 61 2 0 1 25 9 32 0 130 20 1 19 3 0 0 25 1 202 5 5 1 0 24 5 0 14 3 3 0 0 70 0 7 37 94 0
FUN_000001 2 ntLink_0 + 1861 1941 46 3 3 52 22 5 0 5 8 16 34 3 116 14 1 6 0 1 3 12 0 161 14 2 0 5 26 0 0 12 11 2 0 4 59 0 0 30 65 0
FUN_000001 3 ntLink_0 + 2762 2839 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
FUN_000001 4 ntLink_0 + 5044 7056 34 8 3 23 15 3 27 34 13 25 21 4 48 14 2 0 2 10 7 12 28 89 29 7 5 5 13 0 8 11 5 4 4 11 32 0 24 65 40 13

Porites evermanni

Exon CV

Download Exon CV

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries-molecular-calcification/M-multi-species/output/42-sample-exon-count/peve-cv_matrix.tsv 

Peve_exon_cv (first 4 rows)

gene_id POR-216-TP1 POR-216-TP2 POR-216-TP3 POR-216-TP4 POR-236-TP1 POR-236-TP2 POR-245-TP1 POR-245-TP2 POR-245-TP3 POR-245-TP4 POR-260-TP1 POR-260-TP2 POR-260-TP3 POR-260-TP4 POR-262-TP1 POR-262-TP2 POR-262-TP3 POR-262-TP4 POR-69-TP1 POR-69-TP2 POR-69-TP3 POR-69-TP4 POR-72-TP1 POR-72-TP2 POR-72-TP3 POR-72-TP4 POR-73-TP1 POR-73-TP2 POR-73-TP3 POR-73-TP4 POR-74-TP1 POR-74-TP2 POR-74-TP3 POR-74-TP4 POR-83-TP1 POR-83-TP2 POR-83-TP3 POR-83-TP4
gene-Peve_00000003 0.7251225 0.3285807 0.652629 1.3065986 0.5743412 0.5686723 0.7420303 0.7187211 0.5421080 0.8165363 0.4772009 0.5671191 0.7530678 0.6670292 0.8916005 0.5896628 0.4868017 0.4329875 0.8986076 0.5575120 0.5887590 1.046623 0.8814807 1.7813274 0.6817518 0.8243460 0.5275523 1.3684533 0.6164414 0.9365791 0.4046947 0.9433881 0.7996093 1.2041595 0.5622705 1.2605114 1.0063292 1.0110501
gene-Peve_00000005 0.4334701 0.2611595 0.495975 0.5291119 0.2722373 0.2966128 0.3990823 0.4204403 0.4754908 0.3295140 0.3178972 0.3423721 0.2792689 0.2846960 0.4543079 0.4274379 0.4361719 0.3285644 0.4804610 0.2735193 0.3724631 0.464555 0.3105904 0.4118095 0.4278465 0.2674142 0.5008178 0.3034831 0.4442154 0.4994993 0.3730686 0.5149440 0.3879561 0.4014665 0.3323010 0.4470925 0.5444046 0.4869954
gene-Peve_00000006 1.5002239 1.1036268 1.547238 1.3214798 1.3323737 1.5290457 1.1960948 1.0385346 0.8679452 1.3464621 1.0617324 1.5606226 1.3661480 1.5424270 1.3657299 1.2951671 1.2678090 1.6016082 1.2058552 1.0845747 1.1786042 1.253465 1.3801251 1.0428375 0.9158426 1.1641570 1.0119084 1.0421836 1.2049761 0.9661609 1.3326470 1.2978268 0.9565104 1.4769892 1.2212713 1.2145063 1.2502641 1.7391760
gene-Peve_00000011 1.8914687 1.7413367 1.795797 1.4704539 1.7364989 1.4336578 1.6226317 1.5241406 1.8561528 1.2682052 1.1638589 1.9786210 1.3735379 1.5757082 1.6123622 1.8872252 1.4833932 1.7912874 2.2606958 1.5186944 1.8739032 1.914781 1.9840835 2.0484726 1.6848925 1.8362528 1.9929524 1.3339537 1.7366785 1.5142116 1.5896766 1.3842698 1.6548538 1.4355729 2.3132883 2.2811223 1.9783130 2.3879403

Exon Count Matrix

Download Exon Count Matrix

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries-molecular-calcification/M-multi-species/output/40-exon-count-matrix/peve-exon_gene_count_matrix.csv 

Peve_exon_count (first 4 rows)

gene_id e_id chr strand start end POR-216-TP1 POR-216-TP2 POR-216-TP3 POR-216-TP4 POR-236-TP1 POR-236-TP2 POR-245-TP1 POR-245-TP2 POR-245-TP3 POR-245-TP4 POR-260-TP1 POR-260-TP2 POR-260-TP3 POR-260-TP4 POR-262-TP1 POR-262-TP2 POR-262-TP3 POR-262-TP4 POR-69-TP1 POR-69-TP2 POR-69-TP3 POR-69-TP4 POR-72-TP1 POR-72-TP2 POR-72-TP3 POR-72-TP4 POR-73-TP1 POR-73-TP2 POR-73-TP3 POR-73-TP4 POR-74-TP1 POR-74-TP2 POR-74-TP3 POR-74-TP4 POR-83-TP1 POR-83-TP2 POR-83-TP3 POR-83-TP4
gene-Peve_00000001 1 Porites_evermani_scaffold_1 - 3107 3444 0 0 0 0 3 0 0 0 0 0 331 0 6 0 0 3 0 0 0 0 0 0 0 0 0 0 14 1 0 0 0 0 2 4 2 0 1 0
gene-Peve_00000001 2 Porites_evermani_scaffold_1 - 4284 4488 0 0 0 0 0 0 0 0 0 0 43 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 1 0 0 0
gene-Peve_00000002 250 Porites_evermani_scaffold_1 - 424479 425361 7 8 8 4 0 4 14 12 0 5 17 0 3 0 2 6 4 10 1 0 2 0 0 0 0 2 0 4 5 1 2 0 0 0 4 0 0 0
gene-Peve_00000002 251 Porites_evermani_scaffold_1 - 426181 426735 0 5 4 6 0 6 1 0 0 14 14 1 5 0 3 0 3 5 0 0 2 3 0 0 0 1 6 0 3 0 0 5 6 0 6 0 5 1

Pocillopora tuahiniensis

Exon CV

Download Exon CV

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries-molecular-calcification/M-multi-species/output/42-sample-exon-count/ptua-cv_matrix.tsv 

Ptuh_exon_cv (first 4 rows)

gene_id POC-201-TP1 POC-201-TP2 POC-201-TP3 POC-219-TP1 POC-219-TP2 POC-219-TP3 POC-219-TP4 POC-222-TP1 POC-222-TP2 POC-222-TP3 POC-222-TP4 POC-255-TP1 POC-255-TP2 POC-255-TP3 POC-255-TP4 POC-259-TP1 POC-259-TP2 POC-259-TP3 POC-259-TP4 POC-40-TP1 POC-40-TP2 POC-40-TP3 POC-40-TP4 POC-42-TP1 POC-42-TP2 POC-42-TP3 POC-42-TP4 POC-52-TP1 POC-52-TP2 POC-52-TP3 POC-52-TP4 POC-53-TP1 POC-53-TP2 POC-53-TP3 POC-53-TP4 POC-57-TP1 POC-57-TP2 POC-57-TP3 POC-57-TP4
gene-Pocillopora_meandrina_HIv1___RNAseq.10483_t 1.1841672 1.3269516 1.6877936 1.8554407 1.7983556 2.2318398 1.8589386 1.3943541 1.6355111 1.5777909 1.764030 1.2791461 1.4744748 2.316067 1.6647377 1.5445964 1.5322583 2.072337 1.5953003 1.7658246 1.7658383 1.7232639 1.7636723 1.3184004 1.2109251 1.517936 1.7924517 1.562080 1.4323375 1.7130929 1.3999404 1.5500252 1.5112416 1.5672294 1.6315441 1.6506944 1.8471856 1.6496703 1.4749355
gene-Pocillopora_meandrina_HIv1___RNAseq.10568_t 1.0356832 0.9706955 1.1549381 1.0496114 1.0569406 0.5153544 0.9179458 0.8998666 0.8229719 0.6903098 1.054898 1.0398664 0.7969656 1.010574 0.8008383 0.8454713 0.7068676 1.407800 0.8541763 0.4773371 0.7488051 0.6397877 0.8711997 0.5607667 0.8658617 0.913606 0.8842819 0.895092 0.7358446 1.0185661 0.6728081 0.6615746 0.7337614 0.8288398 1.0728251 0.6071959 0.5567480 0.8799199 0.7029411
gene-Pocillopora_meandrina_HIv1___RNAseq.10925_t 0.8530937 0.9528856 1.4518977 1.4007211 1.1199988 1.0111900 1.1572814 0.7980886 0.9468779 0.6111506 1.609263 0.9500079 0.9467207 2.055312 1.2671830 1.2222371 0.7966898 1.098413 1.0107124 0.7920234 0.8497980 0.7740915 1.0965619 0.9151997 0.9088216 1.121206 2.6095647 1.757259 0.8712718 0.9514217 0.7507119 0.7162398 0.7007008 0.8197995 1.1856193 0.6662961 1.3608879 0.7830152 0.9297172
gene-Pocillopora_meandrina_HIv1___RNAseq.10949_t 0.7478408 0.7506053 0.6922207 0.9746087 0.7253771 0.3754997 1.7653871 0.8589661 0.7786004 0.9590317 1.239245 1.0200172 1.9441172 2.449490 0.6669333 1.0326187 1.4338672 1.549411 0.6248311 0.9508638 1.2110383 1.0186531 0.9095838 0.7874763 0.7947567 1.543611 1.2186566 1.673320 0.8828938 0.9070147 0.7276373 0.6618157 0.8360622 1.2694764 0.3390862 1.4050477 0.9520747 0.7801538 1.0179186

Exon Count Matrix

Download Exon Count Matrix

 https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/timeseries-molecular-calcification/M-multi-species/output/40-exon-count-matrix/ptua-exon_gene_count_matrix.csv 

Ptuh_exon_count (first 4 rows)

gene_id e_id chr strand start end POC-201-TP1 POC-201-TP2 POC-201-TP3 POC-219-TP1 POC-219-TP2 POC-219-TP3 POC-219-TP4 POC-222-TP1 POC-222-TP2 POC-222-TP3 POC-222-TP4 POC-255-TP1 POC-255-TP2 POC-255-TP3 POC-255-TP4 POC-259-TP1 POC-259-TP2 POC-259-TP3 POC-259-TP4 POC-40-TP1 POC-40-TP2 POC-40-TP3 POC-40-TP4 POC-42-TP1 POC-42-TP2 POC-42-TP3 POC-42-TP4 POC-52-TP1 POC-52-TP2 POC-52-TP3 POC-52-TP4 POC-53-TP1 POC-53-TP2 POC-53-TP3 POC-53-TP4 POC-57-TP1 POC-57-TP2 POC-57-TP3 POC-57-TP4
gene-Pocillopora_meandrina_HIv1___RNAseq.10273_t 70026 Pocillopora_meandrina_HIv1___Sc0000006 + 4983335 4983993 46 21 12 8 0 0 0 11 3 22 2 2 13 0 9 7 21 11 5 34 13 49 15 30 13 22 0 0 2 0 20 15 10 12 1 3 12 17 11
gene-Pocillopora_meandrina_HIv1___RNAseq.10273_t 70027 Pocillopora_meandrina_HIv1___Sc0000006 + 4985253 4985679 158 12 10 14 15 0 3 23 2 76 14 5 11 15 13 21 35 8 13 19 13 70 20 11 1 16 10 0 0 10 15 30 6 31 0 25 8 51 11
gene-Pocillopora_meandrina_HIv1___RNAseq.10316_t 70272 Pocillopora_meandrina_HIv1___Sc0000006 + 5446327 5446707 59 11 12 0 0 11 26 30 9 141 19 19 2 14 28 7 6 45 32 11 10 110 32 2 0 14 9 0 12 12 32 15 1 428 88 40 6 62 275
gene-Pocillopora_meandrina_HIv1___RNAseq.10316_t 70273 Pocillopora_meandrina_HIv1___Sc0000006 + 5447498 5447708 31 6 2 6 7 1 23 20 7 82 18 2 2 23 29 1 0 7 14 4 9 123 25 2 3 21 0 0 3 6 20 28 1 532 81 32 29 78 221