Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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description Gene Rank Network Comparison Type Filtered green Value Type red network_comparison Interaction Map
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
green
Value Type
red
network_comparison
6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 642 1 19009.7 Squared 16123.9 1.17898
764 4729.12 Measured 4250.18 1.11269
1822 243.085 Ranked 240.32 1.01151
1905 54.4076 Rooted 52.8713 1.02906
6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 643 19012.6 Squared 16126.5 1.17897
763 4729.67 Measured 4250.54 1.11272
1830 243.069 Ranked 240.32 1.01144
1894 54.4127 Rooted 52.8726 1.02913
6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 644 19046 Squared 16156.3 1.17886
759 4736.03 Measured 4254.62 1.11315
1846 54.4715 Rooted 52.887 1.02996
1883 242.881 Ranked 240.317 1.01067
6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 922 31257.4 Squared 27031.3 1.15634
1339 6464.94 Measured 5988.06 1.07964
2041 65.2562 Rooted 63.5421 1.02698
2274 214.801 Ranked 213.642 1.00542
6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 899 34004.2 Squared 29345.7 1.15875
1584 220.432 Ranked 216.891 1.01633
1627 6463.9 Measured 6038.46 1.07046
2366 64.002 Rooted 62.9164 1.01725
6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 0.00001 Measured 0.00001 1
Ranked
Squared
Rooted
60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 1238 26712.4 Squared 23538.3 1.13485
1313 5899.85 Measured 5457.14 1.08112
1830 62.0316 Rooted 60.2038 1.03036
2588 222.64 Ranked 222.305 1.00151
60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 821 65.2371 Rooted 61.3164 1.06394
826 213.912 Ranked 223.186 1.04335
1751 6414.98 Measured 6011.57 1.06711
2621 30796.3 Squared 31749.4 1.03095
60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 1092 232.855 Ranked 226.203 1.02941
2254 24581.5 Squared 22719.3 1.08197
2258 5388.05 Measured 5150.31 1.04616
2720 58.4068 Rooted 58.3416 1.00112
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 233 0 10560 Ranked 9586.97 1.1015
313 6739.34 Measured 6131.07 1.09921
377 47.6722 Rooted 45.8794 1.03908
381 54614.9 Squared 49458.1 1.10427
898 1 238.048 Ranked 229.171 1.03874
2326 22261.9 Squared 20706.1 1.07514
2418 5039.78 Measured 4857.03 1.03763
2564 56.3214 Rooted 56.832 1.00907
60s acidic ribosomal protein p2. [swissprot;acc:p05387] 720 244.435 Ranked 231.92 1.05396
1708 54.3497 Rooted 56.1247 1.03266
2743 4813.92 Measured 4824.49 1.0022
2745 21696.3 Squared 21770.6 1.00342
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 199 0 10545.7 Ranked 11781.8 1.11721
261 24.6198 Rooted 22.315 1.10328

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
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