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 962 to 1011 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
241 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Squared 42411.6 55802.1 1.31573
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Measured 7711.31 6265.76 1.23071
242 j domain containing protein 1. [swissprot;acc:q9ukb3] Ranked 227.357 254.15 1.11785
max protein. [swissprot;acc:p25912] Measured 4640.26 5704.87 1.22943
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Rooted 137.446 120.823 1.13758
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Squared 42411.6 55802.1 1.31573
243 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Measured 4246.95 5208.98 1.22652
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Ranked 227.357 254.15 1.11785
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Squared 42411.6 55802.1 1.31573
trophinin. [swissprot;acc:q12816] Rooted 137.446 120.823 1.13758
244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Ranked 227.357 254.15 1.11785
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 14728.8 19330.8 1.31245
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 146.94 167.046 1.13683
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Measured 4250.14 5211.25 1.22614
245 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Squared 8875.01 6768.05 1.31131
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 4251.65 5212.33 1.22595
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted 146.94 167.046 1.13683
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 226.109 202.333 1.11751
246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Squared 8875.01 6768.05 1.31131
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured 4252.66 5213.05 1.22583
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Rooted 146.94 167.046 1.13683
247 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Squared 8875.01 6768.05 1.31131
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Rooted 47.3621 53.8355 1.13668
rna-binding protein. [refseq;acc:nm_019027] Ranked 237.302 212.41 1.11719
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Measured 6416.68 7865.15 1.22574
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Ranked 237.302 212.41 1.11719
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 8875.01 6768.05 1.31131
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Measured 6417.18 7859.6 1.22477
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted 56.0466 63.4808 1.13264
249 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Squared 8875.01 6768.05 1.31131
ns1-associated protein 1. [refseq;acc:nm_006372] Ranked 237.302 212.41 1.11719
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted 55.5965 62.9349 1.13199
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured 6417.18 7859.59 1.22477
250 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared 69201.8 53013.4 1.30536
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 237.302 212.41 1.11719
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 55.5965 62.9349 1.13199
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured 6417.18 7859.6 1.22477
251 b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 69165.6 52992.1 1.30521
max protein. [swissprot;acc:p25912] Rooted 56.3054 63.7148 1.13159
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Ranked 186.172 166.661 1.11707
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Measured 6417.18 7859.6 1.22477
252 crk-like protein. [swissprot;acc:p46109]
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 212.457 1.11689
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Rooted 51.6736 58.4422 1.13099
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 1.3052
253 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]
mad protein (max dimerizer). [swissprot;acc:q05195] Ranked 228 204.333 1.11583
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 6417.18 7859.59 1.22477

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/