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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 2780 to 2829 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Value Type
network_comparison
red
green
348 Divided 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 1.17914 4991.02 5885.09
Subtracted CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 1013.36 4068.91 5082.27
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 6.9214 59.0296 65.951
SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked 20.346 185.969 165.623
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Squared 6374.6 31248.8 37623.4
349 Divided DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Measured 1.17806 4714.85 5554.38
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Rooted 1.10649 56.0061 61.9704
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Ranked 1.09728 242.14 265.696
SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared 1.24464 35533.9 44227
Subtracted BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 6365.6 34219.8 40585.4
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 20.308 255.112 234.804
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 6.9131 59.029 65.9421
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured 1012.71 3349.9 4362.61
350 Divided ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared 1.24452 35508.7 44191.4
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 1.10643 61.3383 67.8668
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Ranked 1.09728 242.14 265.696
ZNF547 sedlin. [swissprot;acc:o14582] Measured 1.17745 17396.9 20483.9
Subtracted no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Ranked 20.163 233.376 253.539
CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 1011.66 4074.83 5086.49
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 6.8695 59.026 65.8955
ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 6342.6 31583 37925.6
351 Divided no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Measured 1.17745 17396.9 20483.9
ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Rooted 1.10641 61.3352 67.8618
HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared 1.24452 35508.6 44191.3
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Ranked 1.09728 242.14 265.696
Subtracted ADI1 sipl protein. [refseq;acc:nm_018269] Squared 6339.9 30155.1 36495
GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Ranked 20.163 233.376 253.539
NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Measured 1000.81 7878.27 8879.08
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 6.8694 53.5956 60.465
352 Divided no value 40s ribosomal protein s28. [swissprot;acc:p25112] Squared 1.24446 30682.9 38183.6
NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Rooted 1.10641 61.3354 67.8621
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Measured 1.17745 17396.9 20483.9
TXNDC9 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked 1.09728 242.14 265.696
Subtracted no value apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Squared 6310.8 42467.5 36156.7
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked 20.123 237.862 217.739
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 997.37 4911.81 5909.18
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 6.8382 53.607 60.4452
353 Divided GATAD2A p66 alpha. [refseq;acc:nm_017660] Measured 1.17669 12839 10911.1
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 1.09694 231.73 211.252
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Rooted 1.10641 61.3354 67.8623
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 1.24362 71383 57399.3
Subtracted KLF5 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] Measured 997.37 4911.81 5909.18
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 6305.1 34129.7 40434.8
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 6.8335 57.4274 64.2609
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked 20 94 114
354 Divided GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 1.17669 12839 10911.1
PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Squared 1.24352 71360.3 57385.8
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked 1.09694 234.691 257.442
WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 1.10632 49.2848 54.5246
Subtracted CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked 20 94 114

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/