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 Value Type Gene description 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
Value Type
description
red
green
network_comparison
651 Measured ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 5168.43 4597.44 1.1242
Ranked bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 233.725 220.751 1.05877
Squared testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 29012.2 34163.9 1.17757
Rooted programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] 64.5685 69.6269 1.07834
652 Measured short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 5168.43 4597.44 1.1242
Ranked tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] 248.994 235.255 1.0584
Squared chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] 29012.2 34163.9 1.17757
Rooted brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 64.5672 69.6254 1.07834
653 Measured methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 5560.06 6248.27 1.12378
Ranked dok-like protein. [refseq;acc:nm_024872] 216.504 204.622 1.05807
Squared testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 29012.4 34164 1.17757
Rooted arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 64.4927 69.539 1.07825
654 Measured histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 4088.63 4593.43 1.12346
Ranked docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 216.504 204.622 1.05807
Squared sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 27174.1 31992.4 1.17731
Rooted peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 59.9021 64.5838 1.07816
655 Measured dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 4088.63 4593.43 1.12346
Ranked docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 216.504 204.622 1.05807
Squared sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 27174.1 31992.4 1.17731
Rooted hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 59.9021 64.5838 1.07816
656 Measured apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 6139.04 6893.7 1.12293
Ranked tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 216.504 204.622 1.05807
Squared sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 27174.1 31992.4 1.17731
Rooted single-minded homolog 1. [swissprot;acc:p81133] 59.9021 64.5838 1.07816
657 Measured rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 6079.26 6824.47 1.12258
Ranked synapsin iii. [swissprot;acc:o14994] 229.072 216.576 1.0577
Squared sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 27174.1 31992.4 1.17731
Rooted vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 64.75 69.8065 1.07809
658 Measured apical-like protein (apxl protein). [swissprot;acc:q13796] 6088.77 6834.87 1.12254
Ranked aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 229.072 216.576 1.0577
Squared similar to trna synthetase class ii. [refseq;acc:nm_152268] 22293.8 26242.6 1.17713
Rooted eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 52.7523 56.8686 1.07803
659 Measured shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 6089.21 6835.34 1.12253
Ranked 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] 229.072 216.576 1.0577
Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 24614 28973.4 1.17711
Rooted 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 51.7081 47.9816 1.07767
660 Measured u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] 5575.18 6254.85 1.12191
Ranked actin binding lim protein 2. [refseq;acc:nm_032432] 229.072 216.576 1.0577
Squared nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 33024.9 38867.8 1.17692
Rooted fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 133.216 123.627 1.07756
661 Measured step ii splicing factor slu7. [refseq;acc:nm_006425] 5575.18 6254.85 1.12191
Ranked hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] 229.072 216.576 1.0577
Squared delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] 22223.1 26152.4 1.17681
Rooted nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 68.8243 74.1496 1.07738
662 Measured partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 6374.65 7145.59 1.12094
Ranked synapsin ii. [swissprot;acc:q92777] 229.072 216.576 1.0577
Squared ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] 23947.4 28163.7 1.17607
Rooted nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] 68.8237 74.1484 1.07737
663 Measured tubby protein homolog. [swissprot;acc:p50607] 6374.65 7145.59 1.12094
Ranked mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] 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/