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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6658 to 6707 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1665 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Measured 5791.14 6193.02 1.0694
mesoderm induction early response 1. [refseq;acc:nm_020948] Squared 29813.9 32974.4 1.10601
zinc finger protein gli3. [swissprot;acc:p10071] Rooted 54.1965 56.0231 1.0337
1666 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Measured 5791.14 6193.02 1.0694
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Ranked 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
1667 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Ranked 214.898 211.898 1.01416
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Measured 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
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Squared 25005.2 27654.4 1.10595
1668 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Ranked 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 gli2 (tax helper protein). [swissprot;acc:p10070] Rooted 54.1965 56.0231 1.0337
1669 myelin p2 protein. [swissprot;acc:p02689] Measured 5791.14 6193.02 1.0694
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Rooted 98.0116 94.8261 1.03359
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Ranked 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 kelch-like protein 8. [swissprot;acc:q9p2g9] Measured 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
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Ranked 228.496 231.729 1.01415
1671 nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Measured 5791.14 6193.02 1.0694
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Rooted 62.1957 64.2842 1.03358
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Squared 21336.3 23595.6 1.10589
1672 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Measured 5791.14 6193.02 1.0694
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Rooted 64.0468 66.1922 1.0335
ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153] Ranked 228.496 231.729 1.01415
tata element modulatory factor (tmf). [swissprot;acc:p82094] Squared 23713.7 26223.8 1.10585
1673 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Measured 5791.14 6193.02 1.0694
dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992] Ranked 228.496 231.729 1.01415
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Rooted 64.2279 66.3791 1.03349
scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680] Squared 23713.7 26223.8 1.10585
1674 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Measured 5791.14 6193.02 1.0694
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Squared 23713.7 26223.8 1.10585
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Rooted 62.9203 65.027 1.03348
survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] Ranked 228.496 231.729 1.01415
1675 ammecr1 protein. [refseq;acc:nm_015365] Squared 23713.7 26223.8 1.10585
probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6] Ranked 228.496 231.729 1.01415
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Measured 5791.14 6193.02 1.0694
similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428] Rooted 62.9203 65.027 1.03348
1676 elongation factor 2 (ef-2). [swissprot;acc:p13639] 60.3002 62.3124 1.03337
importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Ranked 218.691 215.645 1.01413
indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Measured 5791.14 6193.02 1.0694
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Squared 23713.7 26223.8 1.10585
1677 glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] Ranked 218.654 221.732 1.01408
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Rooted 60.3002 62.3124 1.03337
nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Squared 17043.8 18846.2 1.10575

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/