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 1630 to 1679 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
815 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
832 guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] 4489.72 4965.35 1.10594
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 5929.48 6531.48 602
833 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 5929.55 6531.52 601.97
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Divided 4489.72 4965.35 1.10594
834 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 5623.18 6218.77 1.10592
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted 5929.55 6531.52 601.97
835 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Divided 5623.18 6218.77 1.10592
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Subtracted 5929.61 6531.55 601.94
836 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Divided 4049 4477.43 1.10581
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Subtracted 6229.69 6829.58 599.89
837 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Divided 4063.64 4492.98 1.10565
kinesin family member c3. [refseq;acc:nm_005550] Subtracted 5995.49 6595.35 599.86
838 glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] 6520.28 7119.28 599
pbk1 protein. [sptrembl;acc:o76021] Divided 4064.23 4493.36 1.10559
839 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 7093.86 7842.67 1.10556
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Subtracted 6520.28 7119.28 599
840 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 10300 9701.33 598.67

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/