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.


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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 5786 to 5835 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1447 iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Measured 5117.85 5510.45 1.07671
triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098] Rooted 62.5225 64.9556 1.03892
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Squared 15810.1 17678.6 1.11818
1448 ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2] Rooted 62.5225 64.9556 1.03892
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Ranked 226.532 222.117 1.01988
dpy-30-like protein. [swissprot;acc:q9c005] Measured 5602.01 6031.05 1.07659
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Squared 20900.3 23366.9 1.11802
1449 lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571] Rooted 62.5225 64.9556 1.03892
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Measured 5602.01 6031.05 1.07659
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Squared 15509.6 17339.5 1.11798
transportin-sr; importin 12. [refseq;acc:nm_012470] Ranked 225.305 229.766 1.0198
1450 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 221.804 226.194 1.01979
gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Measured 5602.01 6031.05 1.07659
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Squared 49941.4 44680.1 1.11775
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Rooted 62.5225 64.9556 1.03892
1451 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Squared 26952.5 30122.8 1.11763
my016 protein. [sptrembl;acc:q9h3k6] Ranked 224.755 229.2 1.01978
neighbor of cox4. [swissprot;acc:o43402] Measured 5602.01 6031.05 1.07659
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Rooted 62.5225 64.9556 1.03892
1452 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Ranked 160.381 163.554 1.01978
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Squared 26952.5 30122.8 1.11763
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Measured 5602.01 6031.05 1.07659
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Rooted 67.0522 69.6575 1.03885
1453 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Squared 26952.5 30122.8 1.11763
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Measured 5602.01 6031.05 1.07659
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Ranked 207.038 211.13 1.01976
sipl protein. [refseq;acc:nm_018269] Rooted 66.3152 68.8865 1.03877
1454 lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] 60.3015 62.6383 1.03875
megf6 (fragment). [sptrembl;acc:o75095] Squared 30407.3 33976.9 1.11739
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Ranked 207.024 211.089 1.01964
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Measured 5770.74 6210.65 1.07623
1455 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Squared 15587.6 17417.4 1.11739
eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Ranked 207.024 211.085 1.01962
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Measured 5672.68 6104.68 1.07615
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Rooted 68.657 71.3161 1.03873
1456 dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Squared 18356 20509.7 1.11733
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Measured 5672.25 6104.01 1.07612
eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Ranked 207.024 211.086 1.01962
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] Rooted 68.657 71.3161 1.03873
1457 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Measured 5672.23 6103.98 1.07612
eh-domain containing protein 2. [swissprot;acc:q9nzn4] Ranked 207.024 211.086 1.01962
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Squared 18356 20509.7 1.11733
vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Rooted 68.657 71.3161 1.03873
1458 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
eh-domain containing protein 3. [swissprot;acc:q9nzn3] Ranked 207.024 211.086 1.01962
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Measured 5672.25 6104.01 1.07612
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Squared 25476.6 28464.6 1.11728
1459 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] Measured 5672.25 6104.01 1.07612
adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Rooted 68.657 71.3161 1.03873
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Ranked 192.336 188.637 1.01961

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/