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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2780 to 2829 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
348 GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Squared Divided 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
SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked Subtracted 185.969 165.623 20.346
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Squared 31248.8 37623.4 6374.6
349 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 34219.8 40585.4 6365.6
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 255.112 234.804 20.308
DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Measured Divided 4714.85 5554.38 1.17806
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted Subtracted 59.029 65.9421 6.9131
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 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
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured Subtracted 3349.9 4362.61 1012.71
350 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 233.376 253.539 20.163
ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared Divided 35508.7 44191.4 1.24452
CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured Subtracted 4074.83 5086.49 1011.66
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 59.026 65.8955 6.8695
ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 6342.6
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 Divided 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]
ADI1 sipl protein. [refseq;acc:nm_018269] Squared Subtracted 30155.1 36495 6339.9
ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Rooted Divided 61.3352 67.8618 1.10641
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 Subtracted 233.376 253.539 20.163
HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared Divided 35508.6 44191.3 1.24452
NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Measured Subtracted 7878.27 8879.08 1000.81
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Ranked Divided 242.14 265.696 1.09728
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted Subtracted 53.5956 60.465 6.8694
352 no value 40s ribosomal protein s28. [swissprot;acc:p25112] Squared Divided 30682.9 38183.6 1.24446
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Subtracted 42467.5 36156.7 6310.8
NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Rooted Divided 61.3354 67.8621 1.10641
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Ranked Subtracted 237.862 217.739 20.123
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 4911.81 5909.18 997.37
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.607 60.4452 6.8382
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Measured Divided 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
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 Subtracted 4911.81 5909.18 997.37
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Rooted Divided 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
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Subtracted 34129.7 40434.8 6305.1
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 64.2609 6.8335
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked 94 114 20
354 CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]
EGFL8 palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] Rooted 50.272 43.4634 6.8086
GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured Divided 12839 10911.1 1.17669
PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Squared Subtracted 34129.6 40434.5 6304.9
PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] Divided 71360.3 57385.8 1.24352

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/