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 13314 to 13363 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1665 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Squared Subtracted 28996.8 31444 2447.2
fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Measured Divided 5791.14 6193.02 1.0694
gtp binding protein 2. [refseq;acc:nm_019096] Ranked Subtracted 216.899 213.889 3.01
mesoderm induction early response 1. [refseq;acc:nm_020948] Squared Divided 29813.9 32974.4 1.10601
protein bap28. [swissprot;acc:q9h583] Measured Subtracted 3956.25 4364.25 408
zinc finger protein gli3. [swissprot;acc:p10071] Rooted Divided 54.1965 56.0231 1.0337
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Subtracted 67.2158 69.3348 2.119
1666 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Ranked 216.899 213.889 3.01
fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Measured Divided 5791.14 6193.02 1.0694
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] Rooted Subtracted 67.2158 69.3348 2.119
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Ranked Divided 218.679 215.612 1.01422
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Rooted 54.1965 56.0231 1.0337
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Squared 29813.9 32974.4 1.10601
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Measured Subtracted 4835.55 5243.23 407.68
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Squared 17170.9 19604 2433.1
1667 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Measured 4835.55 5243.23 407.68
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Ranked Divided 214.898 211.898 1.01416
dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Subtracted 216.899 213.889 3.01
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Measured Divided 5791.14 6193.02 1.0694
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] Rooted 54.1965 56.0231 1.0337
hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282] Subtracted 67.2158 69.3348 2.119
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Squared Divided 25005.2 27654.4 1.10595
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Subtracted 24216.1 26647.5 2431.4
1668 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Measured 5916.13 6321.77 405.64
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Rooted 67.2158 69.3348 2.119
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Ranked 216.899 213.889 3.01
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Divided 228.496 231.729 1.01415
wd-repeat protein 4. [swissprot;acc:p57081] Measured 5791.14 6193.02 1.0694
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Squared 21336.3 23595.6 1.10589
zinc finger protein 207. [swissprot;acc:o43670] Subtracted 24216.1 26647.5 2431.4
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Rooted Divided 54.1965 56.0231 1.0337
1669 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] Ranked Subtracted 216.899 213.889 3.01
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Rooted 67.2158 69.3348 2.119
myelin p2 protein. [swissprot;acc:p02689] Measured Divided 5791.14 6193.02 1.0694
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Rooted 98.0116 94.8261 1.03359
protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Squared Subtracted 29345.2 31776.1 2430.9
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Measured 5917.22 6322.72 405.5
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked Divided 228.496 231.729 1.01415
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Squared 21336.3 23595.6 1.10589
1670 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Measured Subtracted 5917.23 6322.73 405.5
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Squared 21291.9 23721 2429.1
kelch-like protein 8. [swissprot;acc:q9p2g9] Measured Divided 5791.14 6193.02 1.0694
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Squared 24949.9 27591.9 1.10589
nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Rooted 64.4426 66.6072 1.03359
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Subtracted 67.2158 69.3348 2.119
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Ranked Divided 228.496 231.729 1.01415
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Subtracted 216.899 213.889 3.01
1671 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Measured 5917.23 6322.73 405.5
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Squared 21291.9 23721 2429.1
nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426] Ranked Divided 228.496 231.729 1.01415

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/