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 2730 to 2779 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
342 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked 0 10074 10609 1.05311
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Measured 3691.15 3952.59 1.07083
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared 1 70830.5 56822 1.24653
histone h2b. [refseq;acc:nm_175055] Rooted 0 29.6319 31.1848 1.05241
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured 1 20446.1 24136.4 1.18049
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Rooted 49.2715 54.5757 1.10765
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Squared 0 3679.95 3222.24 1.14205
343 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Rooted 1 50.3169 45.4333 1.10749
bystin. [swissprot;acc:q13895] Measured 0 2930.88 3135.76 1.0699
casein kinase i alpha s-like. [refseq;acc:nm_145203] Ranked 8356.31 8788.62 1.05173
conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared 1 70830.5 56822 1.24653
espin. [refseq;acc:nm_031475] 0 3679.78 3222.11 1.14204
histone h2b.e (h2b/e). [swissprot;acc:q99879] Rooted 29.632 31.1848 1.0524
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 1 20446.1 24136.4 1.18049
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked 241.625 265.136 1.0973
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 0 10540.6 10027.6 1.05116
histone h2b.c (h2b/c). [swissprot;acc:q99880] Rooted 29.633 31.1851 1.05238
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 1 20446.1 24136.4 1.18049
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 0 2075.64 2220.68 1.06988
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Squared 1 37226.9 46400.1 1.24641
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 0 3665.1 3211.04 1.14141
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted 1 49.4233 54.7327 1.10743
345 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Ranked 0 11563.7 12151.8 1.05086
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Measured 2113.27 2255.28 1.0672
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted 1 56.2615 62.2958 1.10725
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 1.18049
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Squared 35793 44595.3 1.24592
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 0 354.23 402.944 1.13752
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked 1 242.14 265.697 1.09729
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Rooted 0 30.6431 29.1204 1.05229
346 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Measured 1837.26 1721.76 1.06708
40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 1 241.612 265.119 1.09729
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Squared 0 176989 155919 1.13513
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Rooted 21.4045 20.3439 1.05213
grb2-related adaptor protein. [swissprot;acc:q13588] 1 61.4282 68.0107 1.10716
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Squared 34018.3 42373 1.24559
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Ranked 0 9267.81 9736.2 1.05054
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 1 14229.2 16780.7 1.17931
347 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 0 1491.75 1591.6 1.06693
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Ranked 7670 7311 1.0491
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted 1 66.4284 60.0004 1.10713
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Measured 4991.02 5885.09 1.17914
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Ranked 242.14 265.697 1.09729
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Squared 0 10717.9 12115.3 1.13038
scratch; scratch 1. [refseq;acc:nm_031309] Rooted 21.5021 20.4389 1.05202
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Squared 1 16573.6 20637.8 1.24522
348 ad24 protein. [refseq;acc:nm_022451] Rooted 49.2558 54.5235 1.10695
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked 242.14 265.696 1.09728
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Measured 0 14357.1 13463.1 1.0664

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/