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 3430 to 3479 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
429 tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Measured 0 472.351 485.852 1.02858
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Squared 4841.65 4659.88 1.03901
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Measured 1 6272.91 7226.06 1.15195
430 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 1.21457
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Rooted 54.4927 49.6125 1.09837
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 0 22.1458 22.7768 1.02849
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Ranked 11621.7 11913.4 1.0251
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Measured 10247.8 10535 1.02803
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 1 3804.09 4379.37 1.15123
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Squared 0 366.279 352.536 1.03898
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Ranked 1 227.748 210.888 1.07995
431 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Measured 3849.94 4431.36 1.15102
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Rooted 54.4927 49.6125 1.09837
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Ranked 0 10043.7 9799.17 1.02495
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Squared 14421.3 14982.3 1.0389
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Measured 146.622 150.709 1.02787
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared 1 29096 35338.7 1.21456
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Rooted 0 25.6478 26.3666 1.02803
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Ranked 1 236.245 255.113 1.07987
432 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Squared 29095.3 35337.6 1.21455
endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Ranked 212.547 229.411 1.07934
fibrillin 3. [refseq;acc:nm_032447] 0 930 953 1.02473
glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] Squared 25936.7 26909.5 1.03751
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] Measured 100.5 103.25 1.02736
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Rooted 1 54.4927 49.6125 1.09837
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured 5244.71 6036.27 1.15093
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Rooted 0 12.5074 12.1701 1.02772
433 grancalcin. [swissprot;acc:p28676] Squared 1 29095.7 35338.3 1.21455
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Rooted 54.4927 49.6125 1.09837
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Measured 5244.88 6036.38 1.15091
my016 protein. [sptrembl;acc:q9h3k6] Squared 0 1279.28 1234.42 1.03634
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Ranked 1 212.547 229.411 1.07934
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Rooted 0 13.7373 13.373 1.02724
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] Measured 100.5 103.25 1.02736
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Ranked 772 754 1.02387
434 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Rooted 14.6265 15.0206 1.02694
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Ranked 10028.5 10261.5 1.02323
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Squared 1 18306.1 22230.6 1.21438
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Ranked 212.547 229.411 1.07934
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Measured 0 201 206.5 1.02736
thymic stromal co-transporter. [refseq;acc:nm_033051] Rooted 1 54.4927 49.6125 1.09837
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured 5246.38 6037.37 1.15077
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Squared 0 3778.25 3909.18 1.03465
435 60s ribosomal protein l19. [swissprot;acc:p14118] Rooted 1 50.832 46.3081 1.09769
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] Squared 26598.9 32283.5 1.21372
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Measured 0 5891.28 5737.71 1.02677
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Ranked 8770.94 8574.04 1.02296
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Rooted 14.6265 15.0206 1.02694
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Ranked 1 221.522 205.286 1.07909
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Measured 5233.86 6022.6 1.1507

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/