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 5964 to 6013 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1491 loh1cr12. [refseq;acc:nm_058169] Squared 23620.8 26329.4 1.11467
1492 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Measured 4619.81 4965.45 1.07482
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Rooted 64.4465 66.8769 1.03771
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Ranked 224.159 220.017 1.01883
unr protein. [swissprot;acc:o75534] Squared 23620.8 26329.4 1.11467
1493 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Rooted 66.7295 69.2425 1.03766
deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Measured 6146.36 6606.21 1.07482
dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Squared 12403.8 13821.4 1.11429
pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Ranked 204.146 207.988 1.01882
1494 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Squared 24787.1 27617.1 1.11417
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Rooted 64.4361 66.8581 1.03759
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Measured 4619.81 4965.45 1.07482
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Ranked 204.133 207.967 1.01878
1495 casein kinase i alpha s-like. [refseq;acc:nm_145203] 229.459 225.237 1.01874
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Measured 6362.92 6838.6 1.07476
ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Squared 26974.9 30052.7 1.1141
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Rooted 63.106 65.4699 1.03746
1496 26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] Squared 27295.8 30410 1.11409
adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Rooted 63.0785 65.4409 1.03745
apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Measured 5945.56 6389.63 1.07469
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Ranked 229.459 225.237 1.01874
1497 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Squared 23089.8 25724.2 1.11409
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Ranked 224.476 220.363 1.01866
f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Measured 6339.08 6812.45 1.07467
fibulin-2 precursor. [swissprot;acc:p98095] Rooted 76.496 79.3591 1.03743
1498 40s ribosomal protein s13. [swissprot;acc:q02546] Measured 5414.98 5818.7 1.07456
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] Rooted 64.2624 66.6652 1.03739
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Squared 21291.9 23721 1.11409
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Ranked 224.022 219.924 1.01863
1499 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] Rooted 64.2544 66.6549 1.03736
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Squared 21291.9 23721 1.11409
hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Measured 5798.31 6230.55 1.07455
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Ranked 224.509 220.411 1.01859
1500 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Measured 10075.5 9377.75 1.0744
cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] Ranked 213.398 209.52 1.01851
fidgetin-like 1. [refseq;acc:nm_022116] Rooted 63.2895 65.6523 1.03733
histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Squared 21291.9 23721 1.11409
1501 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 18555.4 20672 1.11407
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Measured 10075.5 9377.75 1.0744
kinesin family member c3. [refseq;acc:nm_005550] Ranked 214.727 210.838 1.01845
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Rooted 60.5617 62.8214 1.03731
1502 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Measured 10075.5 9377.75 1.0744
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Squared 18555.4 20672 1.11407
uridine kinase-like 1. [swissprot;acc:q9nwz5] Ranked 218.084 214.149 1.01838
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Rooted 64.181 66.575 1.0373
1503 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Squared 18555.4 20672 1.11407
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Measured 10075.5 9377.75 1.0744
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Ranked 242.181 237.834 1.01828
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Rooted 64.181 66.575 1.0373
1504 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Ranked 259.439 254.797 1.01822

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/