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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6858 to 6907 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1715 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Rooted 62.744 64.7668 1.03224
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Ranked 206.549 203.844 1.01327
katanin p60 subunit a 1. [refseq;acc:nm_007044] Squared 16643.4 18369.3 1.1037
1716 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Rooted 62.7467 64.7695 1.03224
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Measured 6070.41 6485.85 1.06844
lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] Squared 26316.4 29038 1.10342
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Ranked 206.522 203.818 1.01327
1717 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Rooted 62.7494 64.7722 1.03224
epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Squared 27288.3 30109.5 1.10338
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Measured 6069.65 6484.94 1.06842
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Ranked 221.058 218.164 1.01327
1718 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Measured 9720.64 9099.1 1.06831
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Squared 24291.6 26802.4 1.10336
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] Ranked 206.251 203.553 1.01325
tcd37 homolog; prune. [refseq;acc:nm_021222] Rooted 62.7464 64.7691 1.03224
1719 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 62.7446 64.7674
helicase (fragment). [sptrembl;acc:q92771] Ranked 187.204 189.679 1.01322
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Squared 24007.5 26484.7 1.10318
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Measured 5458.12 5830.76 1.06827
1720 beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Squared 59318.4 53788.1 1.10282
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Ranked 187.205 189.679 1.01322
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Rooted 70.2606 72.5203 1.03216
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Measured 5458.12 5830.76 1.06827
1721 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Squared 59318.4 53788.1 1.10282
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Ranked 227.125 224.164 1.01321
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Rooted 68.8451 71.0582 1.03215
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Measured 5458.12 5830.76 1.06827
1722 40s ribosomal protein s13. [swissprot;acc:q02546] Ranked 220.899 223.813 1.01319
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Rooted 67.0685 69.2221 1.03211
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Measured 5458.12 5830.76 1.06827
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Squared 25925.4 28590.5 1.1028
1723 60s ribosomal protein l7. [swissprot;acc:p18124] 14660 16166.6 1.10277
cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] Measured 5458.12 5830.76 1.06827
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Rooted 67.0685 69.2221 1.03211
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Ranked 212.36 215.147 1.01312
1724 dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750] Squared 27318.5 30123.9 1.10269
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Rooted 62.3398 64.3408 1.0321
inositol polyphosphate multikinase. [refseq;acc:nm_152230] Ranked 217.676 220.53 1.01311
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Measured 5458.12 5830.76 1.06827
1725 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Ranked 217.676 220.53 1.01311
centaurin gamma 2. [swissprot;acc:q9upq3] Rooted 61.1276 63.0891 1.03209
glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] Measured 6051.06 6463.65 1.06818
similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5] Squared 27318.5 30123.9 1.10269
1726 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Ranked 217.676 220.53 1.01311
dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507] Squared 27318.5 30123.9 1.10269
general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Rooted 61.1276 63.0891 1.03209
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Measured 7048.79 7527.42 1.0679
1727 centaurin gamma 1. [swissprot;acc:q99490] Rooted 61.1276 63.0891 1.03209
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Ranked 210.366 213.118 1.01308
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Measured 6260.43 6685.05 1.06783

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/