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.


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 2601 to 2650 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
651 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Ranked 233.725 220.751 1.05877
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Measured 5168.43 4597.44 1.1242
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Rooted 64.5685 69.6269 1.07834
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Squared 29012.2 34163.9 1.17757
652 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Rooted 64.5672 69.6254 1.07834
chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] Squared 29012.2 34163.9 1.17757
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Measured 5168.43 4597.44 1.1242
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Ranked 248.994 235.255 1.0584
653 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] Rooted 64.4927 69.539 1.07825
dok-like protein. [refseq;acc:nm_024872] Ranked 216.504 204.622 1.05807
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Measured 5560.06 6248.27 1.12378
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Squared 29012.4 34164 1.17757
654 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Ranked 216.504 204.622 1.05807
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Measured 4088.63 4593.43 1.12346
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Rooted 59.9021 64.5838 1.07816
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Squared 27174.1 31992.4 1.17731
655 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Measured 4088.63 4593.43 1.12346
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Ranked 216.504 204.622 1.05807
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Rooted 59.9021 64.5838 1.07816
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Squared 27174.1 31992.4 1.17731
656 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Measured 6139.04 6893.7 1.12293
single-minded homolog 1. [swissprot;acc:p81133] Rooted 59.9021 64.5838 1.07816
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Squared 27174.1 31992.4 1.17731
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Ranked 216.504 204.622 1.05807
657 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Measured 6079.26 6824.47 1.12258
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Squared 27174.1 31992.4 1.17731
synapsin iii. [swissprot;acc:o14994] Ranked 229.072 216.576 1.0577
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Rooted 64.75 69.8065 1.07809
658 apical-like protein (apxl protein). [swissprot;acc:q13796] Measured 6088.77 6834.87 1.12254
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Ranked 229.072 216.576 1.0577
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Rooted 52.7523 56.8686 1.07803
similar to trna synthetase class ii. [refseq;acc:nm_152268] Squared 22293.8 26242.6 1.17713
659 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Rooted 51.7081 47.9816 1.07767
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Ranked 229.072 216.576 1.0577
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Squared 24614 28973.4 1.17711
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Measured 6089.21 6835.34 1.12253
660 actin binding lim protein 2. [refseq;acc:nm_032432] Ranked 229.072 216.576 1.0577
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Rooted 133.216 123.627 1.07756
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Squared 33024.9 38867.8 1.17692
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Measured 5575.18 6254.85 1.12191
661 delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Squared 22223.1 26152.4 1.17681
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Ranked 229.072 216.576 1.0577
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Rooted 68.8243 74.1496 1.07738
step ii splicing factor slu7. [refseq;acc:nm_006425] Measured 5575.18 6254.85 1.12191
662 nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Rooted 68.8237 74.1484 1.07737
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Measured 6374.65 7145.59 1.12094
synapsin ii. [swissprot;acc:q92777] Ranked 229.072 216.576 1.0577
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Squared 23947.4 28163.7 1.17607
663 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 23947.7 28163.9 1.17606
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Ranked 229.072 216.576 1.0577

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/