Background
Methods
Chemicals and reagents
MAA treatment of TM3 cells and RNA analysis
Microarray analysis
Statistical analysis
Motif enrichment analysis
Ingenuity Pathway Analysis, GO enrichment and heat maps
Results
Overall impact of MAA on TM3 cell gene expression
Name | p-value range | No. molecules |
---|---|---|
A. Top Biological Functions: Diseases and Disorders
| ||
Reproductive System Disease | 3.45E-10 - 4.68E-04 | 160 |
Inflammatory Disease | 1.76E-09 - 1.23E-03 | 507 |
Inflammatory Response | 1.18E-08 - 1.77E-03 | 279 |
Connective Tissue Disorders | 5.10E-07 - 1.23E-03 | 44 |
Skeletal and Muscular Disorders | 5.10E-07 - 1.23E-03 | 516 |
B. Molecular and Cellular Functions
| ||
Cellular Movement | 7.17E-12 - 1.81E-03 | 327 |
Cell-To-Cell Signaling and Interaction | 3.03E-11 - 1.53E-03 | 333 |
Cellular Growth and Proliferation | 3.74E-10 - 1.75E-03 | 492 |
Cellular Development | 7.76E-08 - 1.81E-03 | 455 |
Cell Death | 8.78E-07 - 1.69E-03 | 490 |
C. Physiological System Development and Function
| ||
Tissue Development | 3.47E-10 - 1.53E-03 | 353 |
Cardiovascular System Development & Function | 5.55E-08 - 1.56E-03 | 169 |
Organismal Development | 5.55E-08 - 1.36E-03 | 240 |
Hematological System Development & Function | 7.98E-08 - 1.75E-03 | 348 |
Immune Cell Trafficking | 1.58E-07 - 1.77E-03 | 206 |
D. Associated Network Functions
(top five gene network functions)
| ||
1. Reproductive System Development and Function, Embryonic Development, Tissue Morphology. | ||
2. Infection Mechanism, Dermatological Diseases and Conditions, Organismal Injury and Abnormalities. | ||
3. Carbohydrate Metabolism, Small Molecule Biochemistry, Molecular Transport. | ||
4. Behavior, Nervous System Development and Function, Gene Expression. | ||
5. Cardiovascular System Development and Function, Embryonic Development, Tissue Development. |
Clustering and functional analysis by significance and differential expression
Group | Sub-group | 3 h MAA | 8 h MAA | 24 h MAA | Genes in each subgroup (number) |
---|---|---|---|---|---|
Early (1366 genes)
| early transient up | Up | - | - | 351 |
early transient up | Up | - | Up | 26 | |
early sustained up | Up | Up | - | 149 | |
early persistent up | Up | Up | Up | 223 | |
early transient down | Down | - | - | 245 | |
early transient down | Down | - | Down | 20 | |
early sustained down | Down | Down | - | 198 | |
early persistent down | Down | Down | Down | 154 | |
Mid (1387 genes)
| mid transient up | - | Up | - | 344 |
mid sustained up | - | Up | Up | 466 | |
mid transient down | - | Down | - | 395 | |
mid sustained down | - | Down | Down | 182 | |
Late (1138 genes)
| late up | - | - | Up | 775 |
late down | - | - | Down | 363 |
Response | Top term | Enrich-ment score | Cluster gene count | p-value |
---|---|---|---|---|
Early transient
| GO:0045449, Regulation of transcription | 5.96 | 106 | 3.23E-07 |
GO:0044424, Intracellular part | 5.8 | 211 | 1.11E-06 | |
GO:0065007, Biological regulation | 5.54 | 124 | 6.15E-07 | |
Early sustained
| GO:0050794, Regulation of cellular process | 3.41 | 66 | 1.85E-04 |
IPR000867: Insulin-like growth factor-binding protein, IGFBP | 3.04 | 4 | 6.28E-04 | |
Domain: von Willebrand factor, type C | 2.91 | 4 | 4.81E-04 | |
Early persistent
| GO:0048731, System development | 2.19 | 48 | 1.19E-03 |
GO:0048514, Blood vessel morphogenesis | 2.13 | 9 | 2.17E-03 | |
GO:0044421, Extracellular region part | 2.07 | 43 | 6.46E-03 | |
Mid transient
| GO:0007155, Cell adhesion | 3.11 | 34 | 3.28E-04 |
GO:0044237, Cellular metabolic process | 2.25 | 347 | 1.60E-04 | |
IPR004021: HIN-200/IF120x | 2.13 | 5 | 9.10E-04 | |
Mid sustained
| GO:0044421, Extracellular region part | 8.22 | 109 | 7.30E-10 |
IPR015493: Protocadherin beta | 6.56 | 15 | 1.68E-12 | |
IPR003128: Villin headpiece | 4.39 | 5 | 2.85E-05 | |
Late
| GO:0044421, Extracellular region part | 10.34 | 165 | 5.60E-12 |
GO:0048856, Anatomical structure development | 4.4 | 144 | 1.10E-05 | |
GO:0044449, Contractile fiber part | 3.47 | 12 | 1.75E-04 |