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 3858 to 3907 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
483 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Squared Subtracted 31406.6 36662.8 5256.2
histone h2b.d (h2b/d). [swissprot;acc:q99877] Rooted Divided 50.6084 55.2961 1.09263
neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681] Measured 9649.61 11053.5 1.14549
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Rooted Subtracted 62.7424 67.9648 5.2224
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Ranked Divided 237.109 254.667 1.07405
solute carrier family 13, member 2 (renal sodium/dicarboxylate cotransporter) (na(+)/dicarboxylate cotransporter 1) (nadc-1). [swissprot;acc:q13183] Squared 26867.3 32335.2 1.20352
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] Ranked Subtracted 228.051 212.321 15.73
484 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Divided 237.109 254.667 1.07405
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Squared Subtracted 31406.6 36662.8 5256.2
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Rooted Divided 50.6084 55.2961 1.09263
limkain b1. [refseq;acc:nm_019081] Subtracted 62.7424 67.9648 5.2224
neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297] Measured Divided 9649.61 11053.5 1.14549
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Ranked Subtracted 228.051 212.321 15.73
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Measured 7139.5 7994.06 854.56
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Squared Divided 26867.2 32335 1.20351
485 60s ribosomal protein l18. [swissprot;acc:q07020] Ranked 237.109 254.667 1.07405
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Measured Subtracted 1881.02 1027.36 853.66
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Ranked 231.276 215.627 15.649
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Rooted 62.7424 67.9648 5.2224
solute carrier family 13, member 1 (renal sodium/sulfate cotransporter) (na(+)/sulfate cotransporter) (hnasi-1). [swissprot;acc:q9bzw2] Squared Divided 26867.2 32335 1.20351
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0] Measured 9649.61 11053.5 1.14549
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Rooted 50.6084 55.2961 1.09263
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Squared Subtracted 31401.8 36655.7 5253.9
486 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Rooted 62.7424 67.9648 5.2224
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Ranked 248.866 233.287 15.579
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Measured 5975.11 6826.24 851.13
histone h2b.e (h2b/e). [swissprot;acc:q99879] Rooted Divided 50.6084 55.2961 1.09263
mct-1 protein. [refseq;acc:nm_014060] Ranked 226.313 243.03 1.07387
secretory carrier-associated membrane protein 2. [swissprot;acc:o15127] Squared 26865.9 32332.9 1.20349
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Measured 10908.6 12491.8 1.14513
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Squared Subtracted 25310.2 30537 5226.8
487 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Rooted 62.7424 67.9648 5.2224
malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] Ranked 238.529 254.099 15.57
mitochondrial ribosomal protein l22. [refseq;acc:nm_014180] Divided 226.313 243.03 1.07387
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Measured 5277.4 6042.88 1.14505
secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Squared 26865.9 32332.9 1.20349
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] Measured Subtracted 5975.11 6826.24 851.13
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Rooted Divided 50.0015 54.627 1.09251
transducin-like enhancer protein 4. [swissprot;acc:q04727] Squared Subtracted 31298 36502 5204
488 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Measured Divided 10872.4 12447 1.14483
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Rooted 50.4315 46.1703 1.09229
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked Subtracted 82.5916 98.0548 15.4632
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Rooted 62.7424 67.9648 5.2224
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Squared Divided 26866.1 32333.2 1.20349
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Measured Subtracted 7105.27 7953.71 848.44
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Ranked Divided 225.026 209.798 1.07258
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] Squared Subtracted 27516.2 32720 5203.8
489 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Rooted Divided 50.5505 46.2797 1.09228
apg3p; pc3-96 protein. [refseq;acc:nm_022488] Ranked Subtracted 82.5916 98.0548 15.4632
armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Measured 7101.95 7949.85 847.9

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/