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 1758 to 1807 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
440 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Squared 26348.4 31925.8 1.21168
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Rooted 63.2134 69.352 1.09711
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Ranked 231.802 249.983 1.07843
441 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Squared 26348.7 31924.3 1.21161
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Rooted 63.2134 69.352 1.09711
grancalcin. [swissprot;acc:p28676] Measured 6251.96 7192.13 1.15038
grb2-related adaptor protein. [swissprot;acc:q13588] Ranked 223.457 207.222 1.07835
442 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Squared 51286.6 42334.5 1.21146
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Ranked 223.802 207.55 1.0783
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Measured 6251.99 7192.17 1.15038
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Rooted 63.2134 69.352 1.09711
443 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 50.1766 45.7369 1.09707
brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Measured 6252.27 7192.51 1.15038
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Ranked 223.79 207.539 1.0783
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Squared 26472.8 32067.7 1.21135
444 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Rooted 50.1636 45.7275 1.09701
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Ranked 223.801 207.549 1.0783
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Measured 3758.67 4322.87 1.15011
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Squared 58831 48584.2 1.21091
445 ad24 protein. [refseq;acc:nm_022451] Measured 3753.71 4315.95 1.14978
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked 223.801 207.549 1.0783
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Rooted 50.1635 45.7274 1.09701
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Squared 58831 48584.2 1.21091
446 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Rooted 54.9019 60.2111 1.0967
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Ranked 224.049 207.785 1.07827
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Measured 3766.03 4329.37 1.14958
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Squared 29335.6 35515.5 1.21066
447 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Rooted 54.9019 60.2111 1.0967
pescadillo homolog 1. [swissprot;acc:o00541] Measured 3751.14 4310.89 1.14922
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Ranked 224.049 207.785 1.07827
sipl protein. [refseq;acc:nm_018269] Squared 30155.1 36495 1.21024
448 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 20350.3 16816.1 1.21017
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked 228.468 246.338 1.07822
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Measured 6259.3 7190.91 1.14884
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Rooted 50.1671 45.7563 1.0964
449 bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Ranked 228.463 246.33 1.07821
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Squared 20348.5 16817.2 1.20998
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Rooted 50.162 45.7659 1.09606
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Measured 3761.59 4319.69 1.14837
450 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] Squared 31646.1 38288.7 1.2099
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Measured 4889.21 5610.52 1.14753
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Ranked 235.94 218.837 1.07815
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Rooted 50.4595 46.0411 1.09597
451 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 50.268 45.8663
n-myc proto-oncogene protein. [swissprot;acc:p04198] Measured 4889.71 5610.69 1.14745
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked 239.092 257.705 1.07785
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Squared 17543.3 21222.5 1.20972
452 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted 50.4595 46.0415 1.09596
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Ranked 224.161 207.972 1.07784
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Squared 17543.3 21222.5 1.20972

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/