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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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