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 1950 to 1999 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
244 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Squared 0 80.1214 102.556 1.28001
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 1 146.94 167.046 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
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted 0 22.6521 25.1534 1.11042
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Ranked 11867.6 13019 1.09702
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Measured 1 4251.65 5212.33 1.22595
keratin associated protein 1.5. [refseq;acc:nm_031957] 0 1225.09 1079.36 1.13502
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Rooted 1 146.94 167.046 1.13683
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Squared 0 10596.4 8278.87 1.27993
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] Ranked 1 226.109 202.333 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
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 0 7273.2 9308.93 1.27989
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Measured 1 4252.66 5213.05 1.22583
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Ranked 0 10551.6 11573.7 1.09687
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Measured 1225.09 1079.36 1.13502
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Rooted 12.8935 14.3151 1.11026
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 1 146.94 167.046 1.13683
247 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Squared 0 20324.3 15893.2 1.2788
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 8875.01 6768.05 1.31131
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Measured 0 1225.09 1079.36 1.13502
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Ranked 10551.6 11573.7 1.09687
neurocalcin delta. [swissprot;acc:p29554] Rooted 12.8769 11.6055 1.10955
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 1 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
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Rooted 0 30.7397 27.7265 1.10868
keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked 10551.6 11573.7 1.09687
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Measured 1225.09 1079.37 1.135
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 1 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
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Squared 0 42556.5 33335.4 1.27662
249 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 35446.2 27772 1.27633
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 8875.01 6768.05 1.31131
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Rooted 0 23.5797 26.096 1.10671
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Measured 1225.08 1079.37 1.135
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Ranked 10551.6 11573.7 1.09687
ns1-associated protein 1. [refseq;acc:nm_006372] 1 237.302 212.41 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
dc11 protein. [refseq;acc:nm_020186] Rooted 0 23.5797 26.096 1.10671
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Squared 504.762 643.571 1.275
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 1 237.302 212.41 1.11719
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 10551.6 11573.7 1.09687
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Measured 1225.08 1079.37 1.135
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 1 55.5965 62.9349 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/