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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
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 1563 to 1612 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
782 translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Subtracted 6324.31 6948.5 624.19
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Divided 5874.74 6533.33 1.11211
783 cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Subtracted 6289.72 6911.96 622.24
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Divided 5874.78 6533.37 1.1121
784 cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Subtracted 6289.72 6911.96 622.24
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Divided 5874.77 6533.36 1.1121
785 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 4997 5557.17
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Subtracted 6289.72 6911.96 622.24
786 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 6499.89 7121.77 621.88
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Divided 9304.83 10347.3 1.11204
787 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Subtracted 9720.64 9099.1 621.54
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Divided 5890.49 6547.9 1.11161
788 transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Subtracted 6472.38 7092.65 620.27
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Divided 5890.41 6547.81 1.11161
789 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 5890.59 6547.99 1.1116
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Subtracted 6167.33 6785.98 618.65
790 ran-gtp binding protein (fragment). [sptrembl;acc:o60518] 6165.1 6783.01 617.91
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Divided 5890.88 6548.28 1.1116
791 monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Subtracted 6544.26 7159.43 615.17
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Divided 4025.3 4474.3 1.11154
792 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 6772.75 7526.2 1.11125
target of myb protein 1. [swissprot;acc:o60784] Subtracted 5640.79 6255.85 615.06
793 huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 5641.11 6255.99 614.88
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Divided 5036.92 5596.36 1.11107
794 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 6441.17 7154.55 1.11075
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Subtracted 5641.12 6255.99 614.87
795 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Divided 6441.14 7154.13 1.11069
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Subtracted 5641.53 6256.17 614.64
796 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 6362.64 6976.1 613.46
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 6834.54 7590.49 1.11061
797 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Subtracted 6362.64 6976.1 613.46
798 integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Divided 6834.54 7590.49 1.11061
799 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Subtracted 5222.71 5834.57 611.86
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 6834.54 7590.49 1.11061
800 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Subtracted 3583.56 4194.95 611.39
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Divided 6075.55 6746.92 1.1105
801 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 6456.35 7169.75
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Subtracted 779.167 1390.33 611.163
802 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided 6455.66 7168.82 1.11047
803 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Subtracted 779.167 1390.33 611.163
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 6455.02 7167.96 1.11045
804 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 6770.78 7517.97 1.11036
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Subtracted 779.167 1390.33 611.163
805 60s ribosomal protein l39. [swissprot;acc:p02404] Divided 4708.61 5226.71 1.11003
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Subtracted 779.167 1390.33 611.163
806 60s ribosomal protein l18a. [swissprot;acc:q02543] Divided 4708.61 5226.71 1.11003
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Subtracted 779.167 1390.33 611.163

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/