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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1368 to 1417 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
342 RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Ranked 243.5 267.21 1.09737
343 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Rooted 50.3169 45.4333 1.10749
COG7 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared 70830.5 56822 1.24653
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 20446.1 24136.4 1.18049
PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked 241.625 265.136 1.0973
344 no value 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 20446.1 24136.4 1.18049
IDH2 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
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted 49.4233 54.7327 1.10743
345 CMPK 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
DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted 56.2615 62.2958 1.10725
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 1.18049
SH3GL1 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
346 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 34018.3 42373 1.24559
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Rooted 61.4282 68.0107 1.10716
RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 241.612 265.119 1.09729
SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 14229.2 16780.7 1.17931
347 AK3 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
PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Measured 4991.02 5885.09 1.17914
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Squared 16573.6 20637.8 1.24522
TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted 66.4284 60.0004 1.10713
348 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked 242.14 265.696 1.09728
GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Squared 42566.2 52985.3 1.24477
NOC3L ad24 protein. [refseq;acc:nm_022451] Rooted 49.2558 54.5235 1.10695
SF3B2 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 DHX15 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
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Rooted 56.0061 61.9704 1.10649
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Ranked 242.14 265.696 1.09728
SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared 35533.9 44227 1.24464
350 ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 35508.7 44191.4 1.24452
NAV2 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
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Ranked 242.14 265.696 1.09728
ZNF547 sedlin. [swissprot;acc:o14582] Measured 17396.9 20483.9 1.17745
351 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Rooted 61.3352 67.8618 1.10641
HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared 35508.6 44191.3 1.24452
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Ranked 242.14 265.696 1.09728
352 no value 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 30682.9 38183.6 1.24446
NAV1 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
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Measured 17396.9 20483.9 1.17745
TXNDC9 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked 242.14 265.696 1.09728
353 GATAD2A p66 alpha. [refseq;acc:nm_017660] Measured 12839 10911.1 1.17669
GIPC1 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
NAV3 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
NONO 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
354 GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1.17669
PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Squared 71360.3 57385.8 1.24352
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 234.691 257.442 1.09694
WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 49.2848 54.5246 1.10632
355 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured 12839 10911.1 1.17669

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
- Hugo is the HGNC identifier if it exists
- 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/