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 2586 to 2635 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
647 cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Squared 33384.2 39324.9 1.17795
dynein light chain 2. [refseq;acc:nm_080677] Ranked 216.731 229.549 1.05914
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 5167.88 4594.43 1.12481
648 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Ranked 218.227 206.078 1.05895
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Squared 29174 34363.5 1.17788
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Measured 5248.07 5901.72 1.12455
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Rooted 64.5685 69.6269 1.07834
649 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Ranked 233.725 220.751 1.05877
grancalcin. [swissprot;acc:p28676] Rooted 64.5659 69.624 1.07834
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Squared 29173.8 34362.7 1.17786
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Measured 5248.07 5901.72 1.12455
650 chromodomain y-like protein 2. [refseq;acc:nm_152342] Squared 29016.1 34169.2 1.17759
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Measured 8362.81 9402.7 1.12435
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Rooted 64.566 69.6241 1.07834
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Ranked 228.986 216.276 1.05877
651 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 233.725 220.751
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

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/