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Molecule Parameter List for mRNASc | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | | SOCS1_knockout | 67 | Pathway |
SOCS1_knockout | This model was taken from the Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6
This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. This is the knockout version of Jak-Stat pathway in this model the SOCS1 has been knocked out i.e it formation is not shown.
The graphs are almost similar to the graphs as shown in the paper but STAT1n graph has some ambiguities. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in the simulations. |
mRNASc acting as a Molecule in SOCS1_knockout Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | mRNASc | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 0 | 0.0016667 | No | | Cytoplasmic fraction of mRNA transcribed from DNA by STAT1 activation factors Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
mRNASc acting as a Summed Molecule in SOCS1_knockout Network
| Accession Name | Pathway Name | Target | Input | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | dup_mRNASc | mRNASc
| | Duplicate of the mRNAc Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
mRNASc acting as a Substrate in a reaction in SOCS1_knockout Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | mRNA_deg | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 0.0005
(s^-1) | 0
(s^-1) | - | - | Substrate
mRNASc
Product
mRNA_remain
| | Degradation of mRNAc in the cytoplasm. kf = 0.0005uM kb = 0 Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
mRNASc acting as a Product in a reaction in SOCS1_knockout Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | mRNAn_
cytoplasmic_
transport | SOCS1_knockout
Accession No. : 67 | SOCS1_knockout
Pathway No. : 294 | 0.001
(s^-1) | 0
(s^-1) | - | - | Substrate
mRNASn
Product
mRNASc
| | Transport of nucleoplasmic mRNA to the cytoplasm Kf = 0.001 /sec Kb = 0 /sec Appendix, Satoshi Yamada et al 2003 FEBS Letters 534:190-196 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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