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.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 8664 to 8713 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2166 squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Measured 6952.66 7315.06 1.05212
2167 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Squared 14024.2 15210.1 1.08456
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Ranked 215.925 214.481 1.00673
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Measured 3641.62 3461.4 1.05207
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Rooted 60.8609 62.2517 1.02285
2168 hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Measured 4561.75 4799.24 1.05206
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] Ranked 215.929 214.486 1.00673
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Squared 24593.7 26673.3 1.08456
solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] Rooted 60.8609 62.2517 1.02285
2169 60s ribosomal protein l5. [swissprot;acc:p46777] Measured 3639.65 3459.64 1.05203
heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] Rooted 60.8609 62.2517 1.02285
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Ranked 215.925 214.481 1.00673
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Squared 24593.7 26673.3 1.08456
2170 adp-ribosylation factor 4. [swissprot;acc:p18085] Rooted 60.8609 62.2517 1.02285
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Measured 5825.61 6126.74 1.05169
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] Ranked 215.925 214.481 1.00673
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Squared 22799.4 24726.1 1.08451
2171 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 22799.3
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Rooted 60.8609 62.2517 1.02285
phd finger protein 9. [refseq;acc:nm_018062] Measured 5825.61 6126.74 1.05169
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] Ranked 215.925 214.481 1.00673
2172 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]
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Squared 22799.3 24726.1 1.08451
shc transforming protein. [swissprot;acc:p29353] Rooted 60.8609 62.2517 1.02285
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Measured 5825.61 6126.74 1.05169
2173 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] Ranked 215.925 214.481 1.00673
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Measured 3641.4 3462.96 1.05153
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] Squared 22799.4 24726.1 1.08451
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Rooted 60.8609 62.2517 1.02285
2174 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Measured 3641.45 3463.02 1.05152
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] Ranked 215.925 214.481 1.00673
neuronal shc. [refseq;acc:nm_016848] Rooted 60.8609 62.2517 1.02285
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Squared 18928 17453.6 1.08448
2175 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Ranked 210.209 208.808 1.00671
60s ribosomal protein l23a. [swissprot;acc:p29316] Measured 3642.13 3463.88 1.05146
adp-ribosylation factor 1. [swissprot;acc:p32889] Rooted 60.8609 62.2517 1.02285
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Squared 18928.5 17454 1.08448
2176 heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Rooted 60.8609 62.2517 1.02285
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Measured 6674.58 7015.93 1.05114
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Ranked 218.089 216.64 1.00669
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Squared 18927.7 17453.5 1.08446
2177 adp-ribosylation factor 3. [swissprot;acc:p16587] Rooted 60.8609 62.2517 1.02285
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Measured 5887.43 6187.82 1.05102
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Ranked 210.961 209.563 1.00667
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Squared 18927.7 17453.5 1.08446
2178 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Measured 5893.23 6193.33 1.05092
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Ranked 210.961 209.563 1.00667
lamin a/c (70 kda lamin). [swissprot;acc:p02545] Squared 28995.9 31443.3 1.08441
protein sck (fragment). [swissprot;acc:p98077] Rooted 60.8609 62.2517 1.02285
2179 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Squared 28996.8 31444 1.0844

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/