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 5258 to 5307 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
658 apical-like protein (apxl protein). [swissprot;acc:q13796] Measured Divided 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
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Measured Subtracted 4522.71 5233.14 710.43
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Rooted Divided 52.7523 56.8686 1.07803
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Ranked Subtracted 214.256 202.14 12.116
similar to trna synthetase class ii. [refseq;acc:nm_152268] Squared Divided 22293.8 26242.6 1.17713
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Subtracted 20267.8 24644.8 4377
659 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Rooted Divided 51.7081 47.9816 1.07767
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Ranked Subtracted 214.256 202.14 12.116
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] Divided 229.072 216.576 1.0577
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Measured Subtracted 4858.96 5568.85 709.89
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Squared 20259.5 24635.7 4376.2
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Divided 24614 28973.4 1.17711
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Rooted Subtracted 50.3345 45.6718 4.6627
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Measured Divided 6089.21 6835.34 1.12253
660 60s ribosomal protein l34. [swissprot;acc:p49207] Rooted Subtracted 50.3345 45.6718 4.6627
actin binding lim protein 2. [refseq;acc:nm_032432] Ranked Divided 229.072 216.576 1.0577
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Rooted 133.216 123.627 1.07756
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Ranked Subtracted 214.256 202.14 12.116
metastasis-associated protein mta1. [swissprot;acc:q13330] Measured 4864.25 5573.62 709.37
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Squared 20258.6 24634.7 4376.1
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Divided 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 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Subtracted 4869.15 5578.02 708.87
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Squared Divided 22223.1 26152.4 1.17681
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Ranked Subtracted 214.256 202.14 12.116
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Divided 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
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Subtracted 50.3345 45.6718 4.6627
step ii splicing factor slu7. [refseq;acc:nm_006425] Measured Divided 5575.18 6254.85 1.12191
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Squared Subtracted 25911.5 30281.9 4370.4
662 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Measured 6776.85 7485.55 708.7
gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Ranked 214.256 202.14 12.116
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Rooted Divided 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
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Rooted Subtracted 50.3345 45.6718 4.6627
synapsin ii. [swissprot;acc:q92777] Ranked Divided 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
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Measured Subtracted 7937.72 8646.38 708.66
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Ranked Divided 229.072 216.576 1.0577
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Subtracted 214.256 202.141 12.115
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Rooted Divided 68.8197 74.1413 1.07733
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Subtracted 63.17 67.8116 4.6416
sec13-related protein. [swissprot;acc:p55735] Squared 25911.7 30282.1 4370.4
tubby protein homolog. [swissprot;acc:p50607] Measured Divided 6374.65 7145.59 1.12094
664 60s ribosomal protein l3-like. [swissprot;acc:q92901] Rooted Subtracted 50.3313 45.6913 4.64
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Divided 51.6042 55.574 1.07693
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] 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/