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 5308 to 5357 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
825 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Ranked 206.214 197.614 1.04352
826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 1.04335
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Measured 5195.58 5750.34 1.10678
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Rooted 62.9744 66.9825 1.06365
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Squared 21175.9 24598.1 1.16161
827 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 24211.7 28112.8 1.16112
loh1cr12. [refseq;acc:nm_058169] Ranked 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
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Measured 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
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Measured 5745.61 6354.75 1.10602
unr protein. [swissprot;acc:o75534] Ranked 230.087 220.579 1.0431
829 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 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
830 calcyphosine. [swissprot;acc:q13938] Squared 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
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Ranked 231.734 222.222 1.0428
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Rooted 54.1916 57.6307 1.06346
831 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Squared 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
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Measured 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
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Rooted 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
keratin associated protein 9.2. [refseq;acc:nm_031961] Squared 31100.8 36090.1 1.16042
833 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Ranked 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
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Rooted 59.7298 63.5169 1.0634
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Measured 4489.72 4965.35 1.10594
834 60s ribosomal protein l8. [swissprot;acc:p25120] Ranked 231.734 222.222 1.0428
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Measured 5623.18 6218.77 1.10592
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Rooted 62.309 58.5957 1.06337
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Squared 31100.2 36086.5 1.16033
835 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Measured 5623.18 6218.77 1.10592
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Ranked 231.734 222.222 1.0428
keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Squared 31100.2 36086.5 1.16033
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Rooted 120.033 112.905 1.06313
836 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Measured 4049 4477.43 1.10581
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Squared 31100.2 36086.5 1.16033
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Rooted 65.0565 69.1533 1.06297
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Ranked 231.734 222.222 1.0428
837 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Measured 4063.64 4492.98 1.10565
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Squared 31100.2 36086.5 1.16033
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Ranked 231.734 222.222 1.0428
tubby protein homolog. [swissprot;acc:p50607] Rooted 65.0565 69.1533 1.06297
838 keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Squared 31100.1 36086.4 1.16033

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/