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 5808 to 5857 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1452 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
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Squared 25476.6 28464.6 1.11728
1460 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Measured 5696.65 6130.26 1.07612
phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [swissprot;acc:p15259] Squared 25476.6 28464.6 1.11728
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Ranked 205.817 209.851 1.0196
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Rooted 68.657 71.3161 1.03873
1461 9 kda protein. [swissprot;acc:p13994] Measured 5672.25 6104.01 1.07612
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Rooted 60.3015 62.6331 1.03867
reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Ranked 207.019 211.077 1.0196
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Squared 22440.4 25069.1 1.11714
1462 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] Ranked 205.817 209.851 1.0196
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Squared 22440.4 25069.1 1.11714
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Rooted 65.2132 67.7352 1.03867
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Measured 5672.24 6103.99 1.07612
1463 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] Rooted 60.3015 62.6331 1.03867
collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Measured 5672.2 6103.92 1.07611
pnas-18. [sptrembl;acc:q9bzu3] Ranked 161.056 164.211 1.01959
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] Squared 23320.4 26051 1.11709
1464 bag-family molecular chaperone regulator-1 (bcl-2 binding athanogene- 1) (bag-1) (glucocorticoid receptor-associated protein rap46). [swissprot;acc:q99933] Rooted 65.2132 67.7352 1.03867
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Ranked 217.351 213.18 1.01957
wd-repeat protein 3. [swissprot;acc:q9unx4] Squared 15590.3 17415.6 1.11708
zasp protein (fragment). [sptrembl;acc:q9y4z3] Measured 5671.93 6103.49 1.07609
1465 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 5686.74 6119.36 1.07608

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/