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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2758 to 2807 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
345 ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked Divided 242.14 265.697 1.09729
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Squared Subtracted 29160.4 35570.2 6409.8
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Measured 4068.78 5082.18 1013.4
346 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked Divided 241.612 265.119 1.09729
apical-like protein (apxl protein). [swissprot;acc:q13796] Subtracted 231.492 211.136 20.356
grb2-related adaptor protein. [swissprot;acc:q13588] Rooted Divided 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
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted Subtracted 57.9819 64.9302 6.9483
vav proto-oncogene. [swissprot;acc:p15498] Squared 31223.8 37614.3 6390.5
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Measured 4068.78 5082.18 1013.4
347 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted Divided 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
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] Rooted Subtracted 57.9819 64.9302 6.9483
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked 231.481 211.131 20.35
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Squared Divided 16573.6 20637.8 1.24522
transcription factor btf3 homolog 3. [swissprot;acc:q13892] 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

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/