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.


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 [...,...].
Network Comparison Type Value Type Gene green description Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 1818 to 1867 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
green
description
Rank
network_comparison
red
214.467 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 2307 1.00507 215.554
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 1878 1.01075 212.186
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] 1877
nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303] 1879
214.474 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] 2159 1.00675 215.921
214.481 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] 1799 1.01182 217.016
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] 2166 1.00673 215.925
calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] 2172
calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] 2173
calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] 2162
calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] 2161
dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] 1800 1.0118 217.011
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] 1803
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] 1802
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] 2167 1.00673 215.925
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] 2169
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] 2174
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] 2163
ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] 2165
ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] 2171
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] 2160
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] 2170
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 2164
214.482 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] 1806 1.01178 217.009
alpha-actinin 4 (non-muscle alpha-actinin 4) (f-actin cross linking protein). [swissprot;acc:o43707] 1805 217.008
214.486 mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] 2168 1.00673 215.929
214.493 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] 1437 1.02022 218.829
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] 1436
214.546 u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 589 1.06371 228.215
214.55 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 1480 1.01918 218.664
214.564 cyclin c. [swissprot;acc:p24863] 1812 1.01168 217.071
214.573 r3h domain protein 1. [swissprot;acc:q15032] 1573 1.01646 218.105
214.599 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 2074 1.00804 216.324
214.606 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 2259 1.00569 213.391
214.69 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 1698 1.01367 217.624
hskin17 protein. [refseq;acc:nm_012311] 1697
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] 1700
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1696
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] 1699
214.698 spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] 1846 1.01103 217.066
214.702 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] 1845 1.01106 217.077
214.739 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 1563 1.01648 218.277
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] 1564
214.801 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 2274 1.00542 213.642
214.826 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] 1659 1.01443 217.925
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 1658
214.894 beta-catenin (pro2286). [swissprot;acc:p35222] 801 1.04445 224.445
214.98 af-6 protein. [swissprot;acc:p55196] 1530 1.01746 218.733
215.034 proteasome subunit beta type 4 precursor (ec 3.4.25.1) (proteasome beta chain) (macropain beta chain) (multicatalytic endopeptidase complex beta chain) (proteasome chain 3) (hsn3) (hsbpros26). [swissprot;acc:p28070] 1641 1.01457 218.167
215.097 i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 1162 1.02632 220.758

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/