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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 10764 to 10813 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1346 dna polymerase delta p38 subunit. [refseq;acc:nm_015584] Squared Subtracted 20397.1 23249.1 2852
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Rooted 62.9331 65.5249 2.5918
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Squared Divided 29909.9 33684.3 1.12619
sestrin 3. [swissprot;acc:p58005] Measured Subtracted 5655.85 6120.65 464.8
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Ranked Divided 216.772 221.594 1.02224
1347 aarf domain containing kinase 4. [refseq;acc:nm_024876] Rooted 62.7228 65.296 1.04102
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Squared 14123.5 15905.2 1.12615
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Rooted Subtracted 57.9924 60.5835 2.5911
lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766] Ranked Divided 204.961 209.517 1.02223
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Measured 6153.36 6640.77 1.07921
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Squared Subtracted 30581.7 33431.1 2849.4
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Ranked 218.47 213.876 4.594
sestrin 2 (hi95). [swissprot;acc:p58004] Measured 5655.85 6120.65 464.8
1348 aarf domain containing kinase 1. [refseq;acc:nm_020421] Rooted Divided 62.7228 65.296 1.04102
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Measured Subtracted 5655.85 6120.64 464.79
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Divided 6153.36 6640.77 1.07921
growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Ranked Subtracted 218.47 213.876 4.594
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Squared 20812.4 23659.7 2847.3
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided 29911.6 33682.9 1.12608
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Rooted Subtracted 85.2289 82.6464 2.5825
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Ranked Divided 218.569 213.832 1.02215
1349 40s ribosomal protein s8. [swissprot;acc:p09058] Subtracted 218.64 214.049 4.591
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Rooted Divided 62.138 64.6833 1.04096
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Measured Subtracted 5655.85 6120.64 464.79
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Rooted 85.2289 82.6464 2.5825
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Squared Divided 29911.8 33682.7 1.12607
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Measured 6153.36 6640.77 1.07921
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Squared Subtracted 22959.6 25806.2 2846.6
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Ranked Divided 218.572 213.841 1.02212
1350 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Measured Subtracted 5655.85 6120.64 464.79
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Rooted 61.2224 58.6404 2.582
eyes absent homolog 1. [swissprot;acc:q99502] Ranked 218.463 213.872 4.591
n-myc proto-oncogene protein. [swissprot;acc:p04198] Squared 20816.6 23663.1 2846.5
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Divided 29911.7 33682.8 1.12607
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Rooted 62.1427 64.6863 1.04093
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Measured 6783.78 7320.39 1.0791
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Ranked 218.574 213.847 1.0221
1351 dual specificity mitogen-activated protein kinase kinase 6 (ec 2.7.1.-) (map kinase kinase 6) (mapkk 6) (mapk/erk kinase 6) (sapkk3). [swissprot;acc:p52564] Measured 6105.23 6587.88 1.07906
eyes absent homolog 4. [swissprot;acc:o95677] Ranked Subtracted 218.449 213.864 4.585
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Squared 20823.1 23668.4 2845.3
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Measured 5655.85 6120.64 464.79
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Rooted 61.2224 58.6404 2.582
prohibitin. [swissprot;acc:p35232] Ranked Divided 211.513 206.941 1.02209
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Squared 14753.6 16612.9 1.12602
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Rooted 61.6779 64.2009 1.04091
1352 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Measured Subtracted 5655.85 6120.64 464.79
dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] Divided 6104.11 6586.48 1.07902
ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Squared Subtracted 20823.1 23668.4 2845.3
megf6 (fragment). [sptrembl;acc:o75095] Rooted Divided 61.7068 64.2305 1.0409
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Squared 26925.7 30311.3 1.12574

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/