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 1580 to 1629 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
790 vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Divided 5890.88 6548.28 1.1116
791 monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Subtracted 6544.26 7159.43 615.17
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 4025.3 4474.3 1.11154
792 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 6772.75 7526.2 1.11125
target of myb protein 1. [swissprot;acc:o60784] Subtracted 5640.79 6255.85 615.06
793 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 5641.11 6255.99 614.88
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Divided 5036.92 5596.36 1.11107
794 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 6441.17 7154.55 1.11075
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Subtracted 5641.12 6255.99 614.87
795 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Divided 6441.14 7154.13 1.11069
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Subtracted 5641.53 6256.17 614.64
796 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 6362.64 6976.1 613.46
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 6834.54 7590.49 1.11061
797 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Subtracted 6362.64 6976.1 613.46
798 integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Divided 6834.54 7590.49 1.11061
799 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Subtracted 5222.71 5834.57 611.86
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 6834.54 7590.49 1.11061
800 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Subtracted 3583.56 4194.95 611.39
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Divided 6075.55 6746.92 1.1105
801 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 6456.35 7169.75
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Subtracted 779.167 1390.33 611.163
802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided 6455.66 7168.82 1.11047
803 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Subtracted 779.167 1390.33 611.163
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 6455.02 7167.96 1.11045
804 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 6770.78 7517.97 1.11036
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 779.167 1390.33 611.163
805 60s ribosomal protein l39. [swissprot;acc:p02404] Divided 4708.61 5226.71 1.11003
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted 779.167 1390.33 611.163
806 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 4708.61 5226.71 1.11003
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Subtracted 779.167 1390.33 611.163
807 40s ribosomal protein s19. [swissprot;acc:p39019] Divided 4708.61 5226.71 1.11003
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Subtracted 779.167 1390.33 611.163
808 60s ribosomal protein l31. [swissprot;acc:p12947] Divided 4708.61 5226.71 1.11003
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Subtracted 779.167 1390.33 611.163
809 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 6435.94 7045.75 609.81
wd-repeat protein 3. [swissprot;acc:q9unx4] Divided 4039.81 4484.22 1.11001
810 jm1 protein. [refseq;acc:nm_014008] 5794.8 6427.79 1.10923
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Subtracted 6435.02 7044.65 609.63
811 adiponectin receptor 2. [refseq;acc:nm_024551] 3153.1 3762.56 609.46
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Divided 6000.07 6655.11 1.10917
812 puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Subtracted 5745.61 6354.75 609.14
target of myb protein 1. [swissprot;acc:o60784] Divided 5640.79 6255.85 1.10904
813 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 5641.11 6255.99 1.109
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Subtracted 5745.61 6354.75 609.14
814 dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127]
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Divided 5641.12 6255.99 1.109
815 midasin (midas-containing protein). [swissprot;acc:q9nu22] 4483.08 4971.62 1.10897

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/