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 6508 to 6557 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1627 pp1201 protein. [refseq;acc:nm_022152] Ranked 217.446 214.2 1.01515
1628 26s proteasome non-atpase regulatory subunit 9 (26s proteasome regulatory subunit p27). [swissprot;acc:o00233] Squared 27762.4 30763.9 1.10811
glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] Measured 5920.55 6337.28 1.07039
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Ranked 217.446 214.2 1.01515
ribokinase (ec 2.7.1.15). [swissprot;acc:q9h477] Rooted 65.117 67.3398 1.03414
1629 dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Measured 6158.32 6590.99 1.07026
mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] Squared 27176.8 30113.9 1.10807
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked 217.446 214.2 1.01515
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Rooted 64.0114 66.1969 1.03414
1630 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524] Squared 27176.8 30113.9 1.10807
ataxin 2-binding protein. [swissprot;acc:q9nwb1] Rooted 61.8846 63.9975 1.03414
c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Measured 9903.22 9253.79 1.07018
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Ranked 217.446 214.2 1.01515
1631 brachyury protein (t protein). [swissprot;acc:o15178] Measured 6179.59 6613.15 1.07016
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Ranked 218.789 215.533 1.01511
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Squared 31026.8 34372.7 1.10784
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Rooted 58.8871 56.9439 1.03412
1632 microtubule-associated protein rp/eb family member 3 (protein eb3). [swissprot;acc:q9upy8] Squared 31026.8 34372.6 1.10784
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Ranked 221.934 218.658 1.01498
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Rooted 65.3797 67.6074 1.03407
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Measured 6179.59 6613.15 1.07016
1633 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] 9899.79 9251.2 1.07011
fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Rooted 61.2707 63.3571 1.03405
histidine-rich membrane protein ke4. [swissprot;acc:q92504] Squared 31026.9 34372.4 1.10783
zinc finger protein 207. [swissprot;acc:o43670] Ranked 221.934 218.658 1.01498
1634 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Rooted 61.2707 63.3571 1.03405
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Ranked 215.772 212.596 1.01494
microtubule-associated protein rp/eb family member 1 (apc-binding protein eb1). [swissprot;acc:q15691] Squared 31026.9 34372.4 1.10783
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Measured 9899.73 9251.16 1.07011
1635 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Squared 27290.4 30221.1 1.10739
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Measured 9899.73 9251.16 1.07011
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Rooted 61.2707 63.3571 1.03405
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Ranked 215.772 212.596 1.01494
1636 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Squared 28554.8 31619.6 1.10733
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Ranked 202.358 199.408 1.01479
wd-repeat protein 4. [swissprot;acc:p57081] Rooted 61.2707 63.3571 1.03405
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Measured 9899.73 9251.16 1.07011
1637 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Ranked 202.358 199.408 1.01479
hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] Squared 12067.6 13362.6 1.10731
myelin p2 protein. [swissprot;acc:p02689] Rooted 61.2707 63.3571 1.03405
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Measured 6112.4 6540.73 1.07008
1638 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 9895.77 9248.18 1.07002
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Squared 12067.6 13362.6 1.10731
kelch-like protein 8. [swissprot;acc:q9p2g9] Rooted 61.2707 63.3571 1.03405
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Ranked 220.686 217.481 1.01474
1639 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Squared 12067.6 13362.6 1.10731
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Rooted 61.2707 63.3571 1.03405
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Measured 5939.71 6354.79 1.06988
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Ranked 194.516 197.364 1.01464
1640 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Measured 7444.28 7964 1.06981

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/