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 1613 to 1662 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
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
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Subtracted 5786.67 6395.78 609.11
816 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Divided 5641.53 6256.17 1.10895
817 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] Subtracted 5657.53 6263.02 605.49
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Divided 6811.2 7547.35 1.10808
818 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 6807.78 7543.28 1.10804
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Subtracted 5657.53 6263.02 605.49
819 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 5912.84 6517.69 604.85
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Divided 6805.45 7540.5 1.10801
820 ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 6805.86 7540.99
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Subtracted 5912.84 6517.69 604.85
821 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Divided 6257.99 6932.95 1.10786
822 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Subtracted 4811.02 5414.64 603.62
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Divided 6311.6 6989.33 1.10738
823 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Subtracted 4810.85 5414.23 603.38
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Divided 6311.83 6989.6 1.10738
824 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 5657.53 6263.02 1.10702
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Subtracted 4810.85 5414.23 603.38
825 atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Divided 5657.53 6263.02 1.10702
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Subtracted 4810.85 5414.22 603.37
826 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Divided 5195.58 5750.34 1.10678
peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] Subtracted 4810.85 5414.21 603.36
827 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 4810.71 5413.89 603.18
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Divided 5172.07 5723.22 1.10656
828 puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] 5745.61 6354.75 1.10602
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Subtracted 5903.18 6506.32 603.14
829 leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Divided 5745.61 6354.75 1.10602
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 5903.18 6506.32 603.14
830 dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Divided 5745.61 6354.75 1.10602
lbp-9. [refseq;acc:nm_014553] Subtracted 5903.18 6506.32 603.14
831 splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152]
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Divided 4062.03 4492.48 1.10597

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/