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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Rank Gene description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 851 to 900 of 3730 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
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] 0 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
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 0 9141.6 8940.14 1.02253
444 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 14556.7 14237.8 1.0224
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 1 223.801 207.549 1.0783
445 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 0 7965.06 7790.78 1.02237
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 1 223.801 207.549 1.0783
446 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] 0 7965.06 7790.78 1.02237
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 1 224.049 207.785 1.07827
447 protein hspc134 (protein cda04). [swissprot;acc:q9by43] 0 12532.2 12808.8 1.02207
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] 1 224.049 207.785 1.07827
448 microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 228.468 246.338 1.07822
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] 0 2939 2876 1.02191
449 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 9897.12 9690.83 1.02129
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] 1 228.463 246.33 1.07821
450 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.94 218.837 1.07815
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 0 11290.8 11525.8 1.02081

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/