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 red green network_comparison
Results: HTML CSV LaTeX Showing element 1386 to 1435 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
347 Ranked gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 242.14 265.697 1.09729
Squared small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 16573.6 20637.8 1.24522
Rooted cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 66.4284 60.0004 1.10713
348 Measured splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 4991.02 5885.09 1.17914
Ranked adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 265.696 1.09728
Squared golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 42566.2 52985.3 1.24477
Rooted ad24 protein. [refseq;acc:nm_022451] 49.2558 54.5235 1.10695
349 Measured putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 4714.85 5554.38 1.17806
Ranked surfeit locus protein 5. [swissprot;acc:q15528] 242.14 265.696 1.09728
Squared sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 35533.9 44227 1.24464
Rooted u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 56.0061 61.9704 1.10649
350 Measured sedlin. [swissprot;acc:o14582] 17396.9 20483.9 1.17745
Ranked zinc finger protein 291. [swissprot;acc:q9by12] 242.14 265.696 1.09728
Squared armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 35508.7 44191.4 1.24452
Rooted neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 61.3383 67.8668 1.10643
351 Measured synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 17396.9 20483.9 1.17745
Ranked peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 242.14 265.696 1.09728
Squared histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 35508.6 44191.3 1.24452
Rooted e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 61.3352 67.8618 1.10641
352 Measured bet3 homolog. [swissprot;acc:o43617] 17396.9 20483.9 1.17745
Ranked protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 242.14 265.696 1.09728
Squared 40s ribosomal protein s28. [swissprot;acc:p25112] 30682.9 38183.6 1.24446
Rooted neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 61.3354 67.8621 1.10641
353 Measured p66 alpha. [refseq;acc:nm_017660] 12839 10911.1 1.17669
Ranked rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 231.73 211.252 1.09694
Squared 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 71383 57399.3 1.24362
Rooted neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 61.3354 67.8623 1.10641
354 Measured transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 12839 10911.1 1.17669
Ranked syntaxin 10 (syn10). [swissprot;acc:o60499] 234.691 257.442 1.09694
Squared paraspeckle protein 1. [refseq;acc:nm_018282] 71360.3 57385.8 1.24352
Rooted wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 49.2848 54.5246 1.10632
355 Measured tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12839 10911.1 1.17669
Ranked syntaxin 6. [swissprot;acc:o43752] 234.673 257.414 1.09691
Squared sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 15588.1 19381.8 1.24337
Rooted enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 58.0752 64.23 1.10598
356 Measured t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 11004.2 12944.2 1.1763
Ranked 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796 1.09684
Squared sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] 35247.5 43820.5 1.24322
Rooted splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 58.0752 64.23 1.10598
357 Measured imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 5061.11 5950.22 1.17567
Ranked 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 266.661 1.09683
Squared uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 9811.86 7908.29 1.24071
Rooted growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 61.2684 67.755 1.10587
358 Measured microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] 5061.11 5950.22 1.17567
Ranked ribosomal protein l10-like protein. [refseq;acc:nm_080746] 243.12 266.662 1.09683
Squared serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 9811.73 7908.13 1.24071
Rooted 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] 61.2684 67.755 1.10587
359 Measured cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 12798.9 10887.2 1.17559
Ranked 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 1.09678
Squared serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 9812.34 7908.87 1.24068

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/