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 Value Type description Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
green
red
network_comparison
238 Squared neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] 55802.1 42411.6 1.31573
Rooted melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 120.823 137.446 1.13758
239 Measured carboxypeptidase b precursor. [refseq;acc:nm_020361] 6265.8 7711.38 1.23071
Ranked glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 254.15 227.357 1.11785
Squared mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] 55802.1 42411.6 1.31573
Rooted melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 120.823 137.446 1.13758
240 Measured mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 6265.79 7711.36 1.23071
Ranked androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 254.15 227.357 1.11785
Squared mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539] 55802.1 42411.6 1.31573
Rooted melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 120.823 137.446 1.13758
241 Measured plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 6265.76 7711.31 1.23071
Ranked atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 254.15 227.357 1.11785
Squared neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] 55802.1 42411.6 1.31573
Rooted melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 120.823 137.446 1.13758
242 Measured max protein. [swissprot;acc:p25912] 5704.87 4640.26 1.22943
Ranked j domain containing protein 1. [swissprot;acc:q9ukb3] 254.15 227.357 1.11785
Squared neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] 55802.1 42411.6 1.31573
Rooted 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] 120.823 137.446 1.13758
243 Measured homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 5208.98 4246.95 1.22652
Ranked sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 254.15 227.357 1.11785
Squared sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] 55802.1 42411.6 1.31573
Rooted trophinin. [swissprot;acc:q12816] 120.823 137.446 1.13758
244 Measured ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 5211.25 4250.14 1.22614
Ranked ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 254.15 227.357 1.11785
Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 19330.8 14728.8 1.31245
Rooted myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 167.046 146.94 1.13683
245 Measured homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 5212.33 4251.65 1.22595
Ranked small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 202.333 226.109 1.11751
Squared 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 6768.05 8875.01 1.31131
Rooted myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 167.046 146.94 1.13683
246 Measured homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 5213.05 4252.66 1.22583
Ranked eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 212.363 237.312 1.11748
Squared glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 6768.05 8875.01 1.31131
Rooted myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 167.046 146.94 1.13683
247 Measured wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 7865.15 6416.68 1.22574
Ranked rna-binding protein. [refseq;acc:nm_019027] 212.41 237.302 1.11719
Squared glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 6768.05 8875.01 1.31131
Rooted probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 53.8355 47.3621 1.13668
248 Measured proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 7859.6 6417.18 1.22477
Ranked apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 212.41 237.302 1.11719
Squared myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 6768.05 8875.01 1.31131
Rooted u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] 63.4808 56.0466 1.13264
249 Measured tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 7859.59 6417.18 1.22477
Ranked ns1-associated protein 1. [refseq;acc:nm_006372] 212.41 237.302 1.11719
Squared glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 6768.05 8875.01 1.31131
Rooted 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] 62.9349 55.5965 1.13199
250 Measured proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 7859.6 6417.18 1.22477
Ranked heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 212.41 237.302 1.11719
Squared c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 53013.4 69201.8 1.30536
Rooted nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 62.9349 55.5965 1.13199

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/