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 701 to 750 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
351 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Subtracted 7878.27 8879.08 1000.81
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided 17396.9 20483.9 1.17745
352 bet3 homolog. [swissprot;acc:o43617]
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Subtracted 4911.81 5909.18 997.37
353 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]
p66 alpha. [refseq;acc:nm_017660] Divided 12839 10911.1 1.17669
354 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Subtracted 6913.6 7907.05 993.45
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Divided 12839 10911.1 1.17669
355 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Subtracted 4914.27 5907.12 992.85
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Divided 12839 10911.1 1.17669
356 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 11004.2 12944.2 1.1763
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Subtracted 4914.27 5907.12 992.85
357 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Divided 5061.11 5950.22 1.17567
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Subtracted 4977.09 5966.44 989.35
358 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Divided 5061.11 5950.22 1.17567
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted 4977.8 5966.14 988.34
359 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Divided 12798.9 10887.2 1.17559
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 1920.75 2907.43 986.68
360 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Divided 12796.8 10886 1.17553
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Subtracted 4590.18 5575.52 985.34
361 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 6875.08 7858.38 983.3
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Divided 12787.6 10880.5 1.17528
362 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 12786.6 10879.9 1.17525
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Subtracted 4981.52 5964.58 983.06
363 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Divided 12780.7 10876.4 1.17509
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Subtracted 6856.71 7838.3 981.59
364 dok-like protein. [refseq;acc:nm_024872] 6102.59 7081.46 978.87
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Divided 5189 6088.47 1.17334
365 calcyphosine. [swissprot;acc:q13938]
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Subtracted 6102.59 7081.46 978.87
366 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 5189 6088.47 1.17334
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Subtracted 6102.59 7081.46 978.87
367 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 4024.4 4719.35 1.17268
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted 6102.59 7081.46 978.87
368 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Divided 5082.66 5959.99 1.17261
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Subtracted 7756.51 8731.76 975.25
369 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Divided 3583.56 4194.95 1.17061
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Subtracted 7755.69 8730.74 975.05
370 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Divided 4108.15 4808.93 1.17058
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Subtracted 7753.59 8728.13 974.54
371 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 4855.46 5824.52 969.06
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Divided 5067.02 5926.46 1.16961
372 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 5067 5926.17 1.16956
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] Subtracted 4909.79 5878.79 969
373 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Divided 5066.99 5926.1 1.16955
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Subtracted 4682.88 5646.19 963.31
374 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 4246.95 5208.98 962.03
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Divided 5066.93 5925.38 1.16942
375 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 4700.42 5492.63 1.16854
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted 4250.14 5211.25 961.11

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/