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 [...,...].
Gene description Value Type Rank Network Comparison Type red Filtered Interaction Map network_comparison green
Results: HTML CSV LaTeX Showing element 451 to 500 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Value Type
Rank
red
Filtered
network_comparison
green
5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 595 34129.7 1 1.18474 40434.8
Rooted 751 66.9738 1.06704 71.4638
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Measured 686 6920.69 1.11949 7747.63
Ranked 874 212.002 1.03946 203.954
Squared 596 34129.6 1.18473 40434.5
Rooted 749 66.9737 1.06704 71.4637
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Measured 692 6920.69 1.11949 7747.63
Ranked 880 212.002 1.03946 203.954
Squared 601 34129.6 1.18473 40434.5
Rooted 756 66.9737 1.06704 71.4637
5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Measured 690 6920.69 1.11949 7747.63
Ranked 878 212.002 1.03946 203.954
Squared 599 34129.6 1.18473 40434.5
Rooted 754 66.9737 1.06704 71.4637
5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Measured 1606 5232.99 1.07138 5606.53
Ranked 1769 223.016 1.01219 225.734
Squared 1192 21639 1.13743 24612.9
Rooted 2302 59.4004 1.01929 60.5463
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] Measured 57 270.264 0 1.89769 142.417
1229 5998.69 1 1.08519 6509.74
Ranked 288 14930.6 0 1.07517 16053
1021 221.278 1 1.03204 214.409
Squared 65 50.642 0 3.33538 15.1833
2161 30116.4 1 1.08523 32683.2
Rooted 83 10.9038 0 1.34243 8.12243
981 61.9129 1 1.05589 65.3733
5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Measured 1910 6858.84 1.06246 7287.27
Ranked 2491 194.527 1.00284 195.08
Squared 786 27407.7 1.16492 31927.7
Rooted 2312 70.5239 1.0191 71.8706
5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Measured 287 726.245 0 1.11385 808.929
1915 6858.84 1 1.06246 7287.27
Ranked 412 8546.06 0 1.03217 8279.69
2496 194.527 1 1.00284 195.08
Squared 419 202.436 0 1.04915 212.386
791 27407.7 1 1.16492 31927.7
Rooted 335 24.2756 0 1.05406 25.588
2317 70.5239 1 1.0191 71.8706
5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Measured 1833 6175.23 1.06439 6572.85
Ranked 2754 210.638 1.00002 210.642
Squared 1635 27290.4 1.10739 30221.1
Rooted 2095 64.8399 1.0253 66.4806
5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] Measured 1115 5795.13 1.08957 6314.19
Ranked 1921 221.607 1.01012 219.386
Squared 941 26005.2 1.1544 30020.3
Rooted 1362 61.5231 1.04084 64.0358
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] Measured 2028 10243.4 1.05746 9686.82
Ranked 2532 190.405 1.00214 190.812
Squared 353 71383 1.24362 57399.3
Rooted 2636 80.3593 1.00647 79.843

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/