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 1651 to 1700 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
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
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Divided 5786.67 6395.78 1.10526
841 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Subtracted 10300 9701.33 598.67
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Divided 5786.67 6395.78 1.10526
842 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Subtracted 5623.18 6218.77 595.59
loh1cr12. [refseq;acc:nm_058169] Divided 5195.48 5741.63 1.10512
843 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Subtracted 5623.18 6218.77 595.59
unr protein. [swissprot;acc:o75534] Divided 5195.48 5741.63 1.10512
844 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 3641.89 4236.95 595.06
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Divided 6276.97 6934.8 1.1048
845 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Subtracted 5797.88 6391.75 593.87
846 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Divided 5607.43 6194.98 1.10478
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 5797.88 6391.75 593.87
847 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Divided 6776.85 7485.55 1.10458
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Subtracted 5797.88 6391.75 593.87
848 phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] 6441.56 7034.86 593.3
wd-repeat protein bing4. [swissprot;acc:o15213] Divided 4066.56 4491.65 1.10453
849 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 6194.15 6839.37 1.10417
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Subtracted 6439.63 7032.19 592.56
850 propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Divided 6194.15 6839.37 1.10417
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Subtracted 6439.66 7032.22 592.56

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/