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 2775 to 2824 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
347 transcription factor btf3 homolog 3. [swissprot;acc:q13892] Squared Subtracted 34268.1 40650.4 6382.3
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Measured 4068.82 5082.21 1013.39
348 ad24 protein. [refseq;acc:nm_022451] Rooted Divided 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
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
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 59.0296 65.951 6.9214
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Measured Divided 4991.02 5885.09 1.17914
vav-3 protein. [swissprot;acc:q9ukw4] Squared Subtracted 31248.8 37623.4 6374.6
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Measured 4068.91 5082.27 1013.36
349 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 255.112 234.804 20.308
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
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted 3349.9 4362.61 1012.71
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 59.029 65.9421 6.9131
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared Divided 35533.9 44227 1.24464
surfeit locus protein 5. [swissprot;acc:q15528] Ranked 242.14 265.696 1.09728
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Squared Subtracted 34219.8 40585.4 6365.6
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Rooted Divided 56.0061 61.9704 1.10649
350 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Squared 35508.7 44191.4 1.24452
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Subtracted 31583 37925.6 6342.6
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
sedlin. [swissprot;acc:o14582] Measured 17396.9 20483.9 1.17745
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted Subtracted 59.026 65.8955 6.8695
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
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Measured 4074.83 5086.49 1011.66
zinc finger protein 291. [swissprot;acc:q9by12] Ranked Divided 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
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
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Ranked Divided 242.14 265.696 1.09728
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted Subtracted 53.5956 60.465 6.8694
sipl protein. [refseq;acc:nm_018269] Squared 30155.1 36495 6339.9
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Measured Divided 17396.9 20483.9 1.17745
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
352 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
bet3 homolog. [swissprot;acc:o43617] Measured Divided 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
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 237.862 217.739 20.123
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Rooted 53.607 60.4452 6.8382
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured 4911.81 5909.18 997.37
353 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Squared 34129.7 40434.8 6305.1
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] Divided 71383 57399.3 1.24362
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Ranked Subtracted 94 114 20
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 4911.81 5909.18 997.37
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
p66 alpha. [refseq;acc:nm_017660] Measured 12839 10911.1 1.17669
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted Subtracted 57.4274 64.2609 6.8335
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Ranked Divided 231.73 211.252 1.09694

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/