Xenopus at Systems Biology, HMS




This webpage provides supplementary materials for Clustering and browser for "To Be Decided", Peshkin et al., To Be Decided, 2019.






Table of gene sets features




GeneSet / Clusters



Median Dynamicity



In Set



Total In Genome



Total Detected



Total unDetected



Unique in Genome



Unique Detected



Median concentration (nM)



Tissue Specificity






DNA REPLICATION

0.0011
23
30
28
0
23
23
334.8
1.7




ALL PROTEINS

0.00184
5649
11095
7546
8
5536
5641
70.5
1.6




FATTY ACID METABOLISM

0.00066
28
49
40
2
28
26
1033.6
1.62




TRICARBOXYLIC ACID CYCLE

0.0009
26
48
44
2
26
24
1790.5
1.73




PENTOSE PHOSPHATE PATHWAY

0.00067
12
20
14
1
12
11
434.6
1.98




PROTEOSOME

0.00077
35
70
49
5
35
30
843.8
1.5




RNA DEGRADATION

0.00129
33
61
43
6
33
27
196
1.6




SPLICEOSOME

0.00215
108
188
113
24
103
84
116.8
1.58




KEGG PEROXISOME 

0.00095
78
128
75
21
76
57
221.4
1.52




CHROMOSOMAL PASSENGER COMPLEX 

0.0088
11
18
15
3
8
8
60.1
2.15




RNA POLYMERASE

0.00115
21
34
16
6
20
15
98.8
1.48




MITO CARTA MOUSE V2

0.00112
974
1395
882
309
823
665
273.7
1.59




HALLMARK MITOTIC SPINDLE  

0.00312
200
405
192
69
193
131
57.8
1.68




CELL CYCLE

0.00319
101
178
89
41
90
60
59.2
1.76




RIBOSOME

0.00163
76
172
70
33
75
43
2817.2
1.13




OXIDATIVE PHOSPHORYLATION

0.00111
152
207
118
73
104
79
980.6
1.6




LYSOSOME

0.00098
78
126
49
39
68
39
155.9
1.48




GLYCOLYSIS 

0.00166
55
87
49
28
39
27
1940.9
1.93




CHROMATIN

0.0023
146
234
94
82
116
64
42.1
1.61




KEGG ENDOCYTOSIS

0.0024
183
332
113
106
158
77
74.4
1.72




HALLMARK XENOBIOTIC METABOLISM 

0.00128
200
403
111
125
174
75
273.6
1.6




GO PHOSPHATASE

0.00177
180
320
98
117
159
63
57.4
1.64




E3S

0.00214
624
1160
199
470
489
154
24.4
1.6




KINOME

0.00263
694
1172
209
542
426
152
29.6
1.66




COLLAGENS

0.00323
60
123
11
52
52
8
22.7
1.49




EXTRA CELLULAR MATRIX

0.00356
363
766
63
325
316
38
34.4
1.48




LIGANDS

0.00244
722
1353
134
647
541
75
73.9
1.49




RECEPTORS

0.00393
898
1862
89
833
722
65
35.1
1.59




TRANSCRIPTION FACTORS

0.00344
1412
2269
123
1313
1080
99
18.3
1.67




SECRETED FACTORS

0.00474
321
517
11
312
222
9
18
1.73







Zip files for Clustering Data
Zip files of MATLAB source code for clustering data

GeneSet / Clusters	Median Dynamicity	In Set	Total In Genome	Total Detected	Total unDetected	Unique in Genome	Unique Detected	Median concentration (nM)	Tissue Specificity
DNA REPLICATION	0.0011	23	30	28	0	23	23	334.8	1.7
ALL PROTEINS	0.00184	5649	11095	7546	8	5536	5641	70.5	1.6
FATTY ACID METABOLISM	0.00066	28	49	40	2	28	26	1033.6	1.62
TRICARBOXYLIC ACID CYCLE	0.0009	26	48	44	2	26	24	1790.5	1.73
PENTOSE PHOSPHATE PATHWAY	0.00067	12	20	14	1	12	11	434.6	1.98
PROTEOSOME	0.00077	35	70	49	5	35	30	843.8	1.5
RNA DEGRADATION	0.00129	33	61	43	6	33	27	196	1.6
SPLICEOSOME	0.00215	108	188	113	24	103	84	116.8	1.58
KEGG PEROXISOME	0.00095	78	128	75	21	76	57	221.4	1.52
CHROMOSOMAL PASSENGER COMPLEX	0.0088	11	18	15	3	8	8	60.1	2.15
RNA POLYMERASE	0.00115	21	34	16	6	20	15	98.8	1.48
MITO CARTA MOUSE V2	0.00112	974	1395	882	309	823	665	273.7	1.59
HALLMARK MITOTIC SPINDLE	0.00312	200	405	192	69	193	131	57.8	1.68
CELL CYCLE	0.00319	101	178	89	41	90	60	59.2	1.76
RIBOSOME	0.00163	76	172	70	33	75	43	2817.2	1.13
OXIDATIVE PHOSPHORYLATION	0.00111	152	207	118	73	104	79	980.6	1.6
LYSOSOME	0.00098	78	126	49	39	68	39	155.9	1.48
GLYCOLYSIS	0.00166	55	87	49	28	39	27	1940.9	1.93
CHROMATIN	0.0023	146	234	94	82	116	64	42.1	1.61
KEGG ENDOCYTOSIS	0.0024	183	332	113	106	158	77	74.4	1.72
HALLMARK XENOBIOTIC METABOLISM	0.00128	200	403	111	125	174	75	273.6	1.6
GO PHOSPHATASE	0.00177	180	320	98	117	159	63	57.4	1.64
E3S	0.00214	624	1160	199	470	489	154	24.4	1.6
KINOME	0.00263	694	1172	209	542	426	152	29.6	1.66
COLLAGENS	0.00323	60	123	11	52	52	8	22.7	1.49
EXTRA CELLULAR MATRIX	0.00356	363	766	63	325	316	38	34.4	1.48
LIGANDS	0.00244	722	1353	134	647	541	75	73.9	1.49
RECEPTORS	0.00393	898	1862	89	833	722	65	35.1	1.59
TRANSCRIPTION FACTORS	0.00344	1412	2269	123	1313	1080	99	18.3	1.67
SECRETED FACTORS	0.00474	321	517	11	312	222	9	18	1.73