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 836 to 885 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
418 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 1 233.539 253.197 1.08417
419 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 0 16684 17183 1.02991
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 1 233.539 253.197 1.08417
420 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 0 16684 17183 1.02991
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 1 233.539 253.197 1.08417
421 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 0 11186 10866.3 1.02942
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 1 223.202 205.9 1.08403
422 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 0 12581.7 12224.2 1.02925
ras-related protein rab-37. [swissprot;acc:q96ax2] 1 240.287 260.193 1.08284
423 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 0 5905 6073 1.02845
ras-related protein rab-26. [swissprot;acc:q9ulw5] 1 240.287 260.193 1.08284
424 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 0 9562.48 9298.93 1.02834
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] 1 240.287 260.193 1.08284
425 max protein. [swissprot;acc:p25912] 227.828 210.561 1.082
scribble. [refseq;acc:nm_015356] 0 12370.5 12719 1.02817
426 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] 9412.67 9676.67 1.02805
dynactin 4. [refseq;acc:nm_032486] 1 233.142 252.253 1.08197
427 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 0 11276.1 11582.7 1.02719
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] 1 239.977 259.525 1.08146
428 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] 253.852 234.808 1.0811
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 0 11982.7 12301.2 1.02658
429 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 12318.7 12631.5 1.02539
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 1 239.709 259.038 1.08064
430 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 0 11621.7 11913.4 1.0251
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 1 227.748 210.888 1.07995
431 histone deacetylase 2 (hd2). [swissprot;acc:q92769] 0 10043.7 9799.17 1.02495
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 1 236.245 255.113 1.07987
432 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 212.547 229.411 1.07934
fibrillin 3. [refseq;acc:nm_032447] 0 930 953 1.02473
433 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] 1 212.547 229.411 1.07934
trinucleotide repeat containing 15. [refseq;acc:nm_015575] 0 772 754 1.02387
434 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 10028.5 10261.5 1.02323
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] 1 212.547 229.411 1.07934
435 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 0 8770.94 8574.04 1.02296
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 1 221.522 205.286 1.07909
436 histone h2b.d (h2b/d). [swissprot;acc:q99877] 0 8770.82 8574.19 1.02293
paxillin. [swissprot;acc:p49023] 1 221.522 205.286 1.07909
437 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 209.921 226.459 1.07878
histone h2b.s (h2b/s). [swissprot;acc:p57053] 0 8770.41 8574.66 1.02283
438 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 7759.36 7586.42 1.0228
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 1 233.723 216.674 1.07869
439 40s ribosomal protein s9. [swissprot;acc:p46781] 238.986 257.784 1.07866
histone h2b. [refseq;acc:nm_175055] 0 8770.3 8574.79 1.0228
440 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 1 231.802 249.983 1.07843
histone h2b.e (h2b/e). [swissprot;acc:q99879] 0 8770.28 8574.81 1.0228
441 grb2-related adaptor protein. [swissprot;acc:q13588] 1 223.457 207.222 1.07835
histone h2b.c (h2b/c). [swissprot;acc:q99880] 0 8770.14 8574.98 1.02276
442 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 1 223.802 207.55 1.0783
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 0 14570.4 14247.3 1.02268
443 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] 1 223.79 207.539 1.0783

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/