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 5714 to 5763 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1429 serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Squared 30308.5 33930.2 1.11949
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Measured 5880.37 6334.71 1.07726
wd repeat domain 26. [refseq;acc:nm_025160] Ranked 213.351 217.74 1.02057
1430 65 kda yes-associated protein (yap65). [swissprot;acc:p46937] Rooted 61.2938 63.6979 1.03922
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Ranked 187.114 190.925 1.02037
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] Measured 5880.37 6334.71 1.07726
histone h4. [swissprot;acc:p02304] Squared 33111 29578.7 1.11942
1431 9 kda protein. [swissprot;acc:p13994] Rooted 61.2938 63.6979 1.03922
limkain beta 2. [refseq;acc:nm_025140] Measured 5796.03 6243.78 1.07725
syntaxin 7. [swissprot;acc:o15400] Squared 24103.3 26981.1 1.11939
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Ranked 220.987 225.468 1.02028
1432 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Squared 19672.1 22020.5 1.11938
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Rooted 61.2937 63.6977 1.03922
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Measured 5658.58 6095.62 1.07723
1433 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 5692.34 6131.71 1.07719
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Rooted 60.6322 63.0093 1.03921
inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Ranked 220.987 225.468 1.02028
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Squared 14819.2 16587 1.11929
1434 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 19608.8 21947.6 1.11927
myosin viia. [swissprot;acc:q13402] Measured 5759.68 6203.63 1.07708
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Rooted 86.1912 82.9401 1.0392
uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Ranked 220.987 225.468 1.02028
1435 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Rooted 86.1912 82.9401 1.0392
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Squared 21786.2 24380.3 1.11907
myosin vi. [swissprot;acc:q9um54] Ranked 220.987 225.468 1.02028
ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] Measured 5759.68 6203.63 1.07708
1436 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Rooted 86.1912 82.9401 1.0392
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Squared 21782 24375.4 1.11906
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Ranked 218.829 214.493 1.02022
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] Measured 5759.68 6203.63 1.07708
1437 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] Ranked 218.829 214.493 1.02022
glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] Measured 6089.43 6558.02 1.07695
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Squared 21776.6 24369.1 1.11905
zasp protein (fragment). [sptrembl;acc:q9y4z3] Rooted 61.2913 63.6935 1.03919
1438 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Measured 6721.25 7238.34 1.07693
geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Ranked 225.039 229.573 1.02015
putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] Rooted 60.0677 62.4214 1.03918
uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] Squared 23913 26757.8 1.11896
1439 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Measured 5658.8 6093.56 1.07683
fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Ranked 225.039 229.573 1.02015
megf11 protein. [refseq;acc:nm_032445] Rooted 60.599 62.9716 1.03915
1440 inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] Squared 23913 26757.8 1.11896
megf10 protein. [refseq;acc:nm_032446] Rooted 60.5986 62.9711 1.03915
mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Ranked 225.039 229.573 1.02015
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Measured 6522.96 7023.77 1.07678
1441 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Rooted 60.5976 62.9699 1.03915
fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] Ranked 225.039 229.573 1.02015
proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] Measured 6216.12 6693.38 1.07678

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/