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 3558 to 3607 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
445 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Ranked Subtracted 250.858 234.563 16.295
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Rooted Divided 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 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Subtracted 26348.4 31925.8 5577.4
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Rooted 87.1967 92.7545 5.5578
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Measured 4991.02 5885.09 894.07
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Rooted Divided 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
Subtracted 16.264
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Measured Divided 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
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Subtracted 51.8647 46.3161 5.5486
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Squared 26348.7 31924.3 5575.6
pescadillo homolog 1. [swissprot;acc:o00541] Measured Divided 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
Subtracted 16.264
sipl protein. [refseq;acc:nm_018269] Squared Divided 30155.1 36495 1.21024
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Measured Subtracted 4991.02 5885.09 894.07
448 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Squared Divided 20350.3 16816.1 1.21017
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured Subtracted 4987.58 4094.57 893.01
e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Ranked 223.802 207.55 16.252
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Rooted 87.1432 92.6892 5.546
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Squared 28657.6 34208.6 5551
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Ranked Divided 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
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured Subtracted 5061.11 5950.22 889.11
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Squared 28657.6 34208.6 5551
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 46.3281 5.5433
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Ranked 223.801 207.549 16.252
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Measured Divided 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
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Subtracted 28657.6 34208.6 5551
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Measured Divided 4889.21 5610.52 1.14753
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 5061.11 5950.22 889.11
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Ranked 223.801 207.549 16.252
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 235.94 218.837 1.07815
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Rooted Subtracted 51.8717 46.3287 5.543
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Divided 50.4595 46.0411 1.09597
451 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Subtracted 51.8789 46.3416 5.5373
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 50.268 45.8663 1.09597
n-myc proto-oncogene protein. [swissprot;acc:p04198] Measured 4889.71 5610.69 1.14745
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 Subtracted 223.79 207.539 16.251
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Squared 50724.5 45178.9 5545.6
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked Divided 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

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/