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 6612 to 6661 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
827 jm1 protein. [refseq;acc:nm_014008] Ranked Subtracted 219.762 210.806 8.956
loh1cr12. [refseq;acc:nm_058169] Divided 230.087 220.579 1.0431
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Rooted 62.9744 66.9825 1.06365
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Subtracted 4.0081
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Measured Divided 5172.07 5723.22 1.10656
828 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Squared 24211.7 28112.8 1.16112
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Rooted 87.1432 92.6892 1.06364
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Subtracted 62.9744 66.9825 4.0081
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Measured Divided 5745.61 6354.75 1.10602
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Ranked Subtracted 135.087 144.041 8.954
unr protein. [swissprot;acc:o75534] Divided 230.087 220.579 1.0431
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Measured Subtracted 5903.18 6506.32 603.14
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (ec 2.7.1.115) (branched-chain alpha-ketoacid dehydrogenase kinase) (bckdhkin) (bckd-kinase). [swissprot;acc:o14874] Squared 22347.6 26247.3 3899.7
829 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Rooted 50.8036 46.8198 3.9838
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Squared 22337.3 26234.1 3896.8
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Ranked 252.873 261.821 8.948
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] Rooted Divided 54.1916 57.6307 1.06346
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Measured 5745.61 6354.75 1.10602
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Squared 21651.8 25126.3 1.16047
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Ranked 135.844 130.259 1.04288
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Measured Subtracted 5903.18 6506.32 603.14
830 40s ribosomal protein s16. [swissprot;acc:p17008] Rooted 50.8036 46.8198 3.9838
calcyphosine. [swissprot;acc:q13938] Squared Divided 21651.8 25126.3 1.16047
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Measured 5745.61 6354.75 1.10602
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Squared Subtracted 22337.3 26234.1 3896.8
lbp-9. [refseq;acc:nm_014553] Measured 5903.18 6506.32 603.14
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Ranked Divided 231.734 222.222 1.0428
wd-repeat protein 3. [swissprot;acc:q9unx4] Subtracted 243.896 234.96 8.936
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Rooted Divided 54.1916 57.6307 1.06346
831 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Ranked Subtracted 229.171 238.048 8.877
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Rooted 50.8041 46.8218 3.9823
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Squared Divided 21651.8 25126.3 1.16047
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Ranked 231.734 222.222 1.0428
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Rooted 59.7298 63.5169 1.0634
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Squared Subtracted 22336.8 26233.5 3896.7
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Measured 5903.18 6506.32 603.14
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Divided 4062.03 4492.48 1.10597
832 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Ranked 231.734 222.222 1.0428
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Squared Subtracted 22335.8 26232.2 3896.4
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Rooted Divided 59.7298 63.5169 1.0634
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] Measured 4489.72 4965.35 1.10594
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 5929.48 6531.48 602
keratin associated protein 9.2. [refseq;acc:nm_031961] Squared Divided 31100.8 36090.1 1.16042
myelin gene expression factor 2. [refseq;acc:nm_016132] Rooted Subtracted 56.8369 52.8585 3.9784
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Ranked 229.171 238.048 8.877
833 loh1cr12. [refseq;acc:nm_058169] Rooted 57.805 61.7803 3.9753
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Measured 5929.55 6531.52 601.97
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Ranked Divided 231.734 222.222 1.0428
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Squared 21455.4 24895.7 1.16035
surfeit locus protein 1. [swissprot;acc:q15526] Subtracted 22335.8 26232.2 3896.4

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/