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 1375 to 1424 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
344 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Squared 37226.9 46400.1 1.24641
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted 49.4233 54.7327 1.10743
345 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 56.2615 62.2958 1.10725
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 1.18049
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] Squared 35793 44595.3 1.24592
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked 242.14 265.697 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119
grb2-related adaptor protein. [swissprot;acc:q13588] Rooted 61.4282 68.0107 1.10716
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Squared 34018.3 42373 1.24559
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 14229.2 16780.7 1.17931
347 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted 66.4284 60.0004 1.10713
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Measured 4991.02 5885.09 1.17914
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Ranked 242.14 265.697 1.09729
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Squared 16573.6 20637.8 1.24522
348 ad24 protein. [refseq;acc:nm_022451] Rooted 49.2558 54.5235 1.10695
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked 242.14 265.696 1.09728
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Squared 42566.2 52985.3 1.24477
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Measured 4991.02 5885.09 1.17914
349 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
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared 35533.9 44227 1.24464
surfeit locus protein 5. [swissprot;acc:q15528] Ranked 242.14 265.696 1.09728
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Rooted 56.0061 61.9704 1.10649
350 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared 35508.7 44191.4 1.24452
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] Rooted 61.3383 67.8668 1.10643
sedlin. [swissprot;acc:o14582] Measured 17396.9 20483.9 1.17745
zinc finger protein 291. [swissprot;acc:q9by12] Ranked 242.14 265.696 1.09728
351 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Rooted 61.3352 67.8618 1.10641
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared 35508.6 44191.3 1.24452
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Ranked 242.14 265.696 1.09728
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Measured 17396.9 20483.9 1.17745
352 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 30682.9 38183.6 1.24446
bet3 homolog. [swissprot;acc:o43617] Measured 17396.9 20483.9 1.17745
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Rooted 61.3354 67.8621 1.10641
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked 242.14 265.696 1.09728
353 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] Squared 71383 57399.3 1.24362
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Rooted 61.3354 67.8623 1.10641
p66 alpha. [refseq;acc:nm_017660] Measured 12839 10911.1 1.17669
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Ranked 231.73 211.252 1.09694
354 paraspeckle protein 1. [refseq;acc:nm_018282] Squared 71360.3 57385.8 1.24352
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 234.691 257.442 1.09694
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1.17669
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 49.2848 54.5246 1.10632
355 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 58.0752 64.23 1.10598
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Squared 15588.1 19381.8 1.24337
syntaxin 6. [swissprot;acc:o43752] Ranked 234.673 257.414 1.09691
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured 12839 10911.1 1.17669
356 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Ranked 243.24 266.796 1.09684
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared 35247.5 43820.5 1.24322
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Rooted 58.0752 64.23 1.10598
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured 11004.2 12944.2 1.1763

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/