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 5941 to 5990 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1486 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Rooted 79.3006 82.3013 1.03784
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Ranked 207.877 203.989 1.01906
kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Squared 26696.5 29768.6 1.11508
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Measured 5372.25 5775.21 1.07501
1487 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Squared 26696.5 29768.6 1.11508
dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Rooted 62.3212 64.678 1.03782
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Measured 5573.64 5991.58 1.07499
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Ranked 207.877 203.989 1.01906
1488 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Measured 5573.64 5991.58 1.07499
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Ranked 207.877 203.989 1.01906
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Squared 26696.5 29768.6 1.11508
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Rooted 62.3212 64.678 1.03782
1489 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Squared 26277.3 29299.3 1.115
dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] Rooted 62.3212 64.678 1.03782
mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] Ranked 213.251 209.264 1.01905
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Measured 6192.38 6656.34 1.07492
1490 f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] 6340.5 6815.41 1.0749
p28 ing5. [refseq;acc:nm_032329] Squared 26142 29139.6 1.11467
protein cgi-147. [swissprot;acc:q9y3e5] Ranked 221.961 226.186 1.01903
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Rooted 81.8175 78.8388 1.03778
1491 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 100.828 97.1592 1.03776
fidgetin-like 1. [refseq;acc:nm_022116] Measured 6057.46 6510.9 1.07486
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Ranked 217.704 221.839 1.01899
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

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/