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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Value Type description Filtered green red network_comparison Interaction Map Gene Network Comparison Type Rank
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Value Type  : Measured
description
Filtered
green
red
network_comparison
Interaction Map
Network Comparison Type
Rank
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 1 7747.63 6920.69 1.11949 High confidence Divided 686
826.94 Subtracted 503
8915.81 8886.95 1.00325 Low confidence Divided 4961
28.86 Subtracted 4958
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 7747.63 6920.69 1.11949 High confidence Divided 692
826.94 Subtracted 508
8928.03 8903.9 1.00271 Low confidence Divided 4974
24.13 Subtracted 4966
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 7747.63 6920.69 1.11949 High confidence Divided 690
826.94 Subtracted 506
8914.56 8885.23 1.0033 Low confidence Divided 4960
29.33 Subtracted 4957
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 5606.53 5232.99 1.07138 High confidence Divided 1606
373.54 Subtracted 1846
8500.56 8340.85 1.01915 Low confidence Divided 4466
159.71 Subtracted 4381
5'-nucleotidase precursor (ec 3.1.3.5) (ecto-5'-nucleotidase) (5'-nt) (cd73 antigen). [swissprot;acc:p21589] 7971.53 7791.29 1.02313 Divided 3926
180.24 Subtracted 3967
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 0 142.417 270.264 1.89769 High confidence Divided 57
Low confidence 67
127.847 High confidence Subtracted 251
Low confidence 380
1 6509.74 5998.69 1.08519 High confidence Divided 1229
511.05 Subtracted 1152
7979.28 7708.2 1.03517 Low confidence Divided 1329
271.08 Subtracted 1501
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] 7287.27 6858.84 1.06246 High confidence Divided 1910
428.43 Subtracted 1577
8318.83 8052.1 1.03313 Low confidence Divided 1712
266.73 Subtracted 1665
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 0 651.607 583.664 1.11641 Divided 375
67.943 Subtracted 533
808.929 726.245 1.11385 High confidence Divided 287
82.684 Subtracted 315
1 7287.27 6858.84 1.06246 Divided 1915
428.43 Subtracted 1583
8320.42 8054.28 1.03304 Low confidence Divided 1742
266.14 Subtracted 1676
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] 6572.85 6175.23 1.06439 High confidence Divided 1833
397.62 Subtracted 1726
9082.91 8686.89 1.04559 Low confidence Divided 593
396.02 Subtracted 473
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 6314.19 5795.13 1.08957 High confidence Divided 1115
519.06 Subtracted 1094
9650.42 9113.16 1.05895 Low confidence Divided 295
537.26 Subtracted 220
5-oxoprolinase (ec 3.5.2.9) (5-oxo-l-prolinase) (pyroglutamase) (5-opase) (fragment). [swissprot;acc:o14841] 8909.86 8601.93 1.0358 Divided 1247
307.93 Subtracted 982
54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 8297.84 8028.49 1.03355 Divided 1616
269.35 Subtracted 1559

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/