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 5464 to 5513 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1366 trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6] Squared 30488.9 34284.9 1.1245
1367 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470] Rooted 60.8705 63.3375 1.04053
gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616] Squared 30488.9 34284.9 1.1245
megf10 protein. [refseq;acc:nm_032446] Measured 5793.47 6248.71 1.07858
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Ranked 223.887 228.799 1.02194
1368 beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Measured 5793.29 6248.51 1.07858
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Squared 15565.5 17500.6 1.12432
neighbor of cox4. [swissprot;acc:o43402] Rooted 60.8705 63.3375 1.04053
polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Ranked 228.644 223.736 1.02194
1369 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] Measured 5786.71 6241.16 1.07853
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Ranked 228.644 223.736 1.02194
protein c14orf122 (cgi-112). [swissprot;acc:q9y3b6] Rooted 60.8705 63.3375 1.04053
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Squared 22572.9 25377.6 1.12425
1370 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Ranked 205.185 200.784 1.02192
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Rooted 60.8705 63.3375 1.04053
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Squared 22959.6 25806.2 1.12398
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Measured 10231.8 9487.34 1.07847
1371 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] Squared 18598.9 20901.3 1.12379
double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959] Measured 10231.8 9487.34 1.07847
glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Ranked 228.646 223.744 1.02191
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Rooted 62.3839 64.9113 1.04051
1372 dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] Squared 23319.2 26205 1.12375
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Measured 5743.45 6193.45 1.07835
prefoldin subunit 1. [swissprot;acc:o60925] Rooted 62.3839 64.9113 1.04051
suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] Ranked 216.542 211.908 1.02187
1373 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Squared 23319.2 26205 1.12375
glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234] Ranked 216.542 211.908 1.02187
mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Measured 6079.85 6556.07 1.07833
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Rooted 62.3839 64.9113 1.04051
1374 adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235] Squared 23319.2 26205 1.12375
asc-1 complex subunit p100. [refseq;acc:nm_032204] Ranked 216.542 211.908 1.02187
choline dehydrogenase. [refseq;acc:nm_018397] Rooted 62.3839 64.9113 1.04051
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Measured 6079.45 6555.4 1.07829
1375 adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141] Squared 23319.2 26205 1.12375
calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] Measured 6079.45 6555.4 1.07829
fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] Ranked 216.542 211.908 1.02187
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Rooted 63.5941 66.1672 1.04046
1376 calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] Measured 6079.46 6555.41 1.07829
eyes absent homolog 3. [swissprot;acc:q99504] Ranked 218.537 213.91 1.02163
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Rooted 63.5941 66.1672 1.04046
leng5 protein. [refseq;acc:nm_024075] Squared 22386.1 25153.7 1.12363
1377 heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Rooted 61.9851 64.49 1.04041
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Measured 6079.46 6555.4 1.07829
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Ranked 218.471 213.876 1.02148
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Squared 22386.1 25153.7 1.12363
1378 heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943] Rooted 61.9843 64.4891 1.04041
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Squared 22386.1 25153.7 1.12363
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Ranked 218.47 213.876 1.02148
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Measured 6079.45 6555.4 1.07829
1379 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] Ranked 218.47 213.875 1.02148

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/