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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 3580 to 3629 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
448 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Rooted Subtracted 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
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Measured Subtracted 398.5 1281.5 883
452 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Rooted Divided 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
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Squared Subtracted 59318.4 53788.1 5530.3
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 221.522 205.286 16.236
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Rooted 66.0911 71.6061 5.515
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Squared Divided 17543.3 21222.5 1.20972
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Measured Subtracted 398.5 1281.5 883
zinc finger-like protein 9. [refseq;acc:nm_033414] Divided 3760.8 4315.06 1.14738
453 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Squared Subtracted 59318.4 53788.1 5530.3
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Rooted 66.1583 71.6729 5.5146
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Measured 398.5 1281.5 883
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Divided 3760.8 4315.06 1.14738
paxillin. [swissprot;acc:p49023] Ranked Subtracted 221.522 205.286 16.236
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared Divided 31620.5 38250.7 1.20968
surfeit locus protein 5. [swissprot;acc:q15528] Rooted 50.4595 46.0413 1.09596
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Ranked 224.161 207.972 1.07784
454 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Squared Subtracted 50598.8 45106.3 5492.5
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Rooted 61.1902 66.6503 5.4601
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Measured 398.5 1281.5 883
grb2-related adaptor protein. [swissprot;acc:q13588] Ranked 223.457 207.222 16.235

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/