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 6308 to 6357 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1577 sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Rooted 61.9705 64.1938 1.03588
1578 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Squared 28606.1 31783.4 1.11107
mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Ranked 222.585 218.982 1.01645
proteasome subunit alpha type 4 (ec 3.4.25.1) (proteasome component c9) (macropain subunit c9) (multicatalytic endopeptidase complex subunit c9) (proteasome subunit l). [swissprot;acc:p25789] Measured 6213.27 6659.39 1.0718
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Rooted 61.9701 64.1935 1.03588
1579 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 61.9705 64.1938
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Measured 5842.44 6261.87 1.07179
cda11 protein. [refseq;acc:nm_032026] Ranked 213.181 209.732 1.01644
hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Squared 26462.3 29398.2 1.11095
1580 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 27757.8 30834 1.11082
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Rooted 61.9705 64.1938 1.03588
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Ranked 168.018 170.769 1.01637
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Measured 6376.12 6833.59 1.07175
1581 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263]
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Ranked 168.002 170.753 1.01637
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Squared 41510.6 37375.2 1.11065
phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Rooted 61.9704 64.1937 1.03588
1582 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] 61.9701 64.1935
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Ranked 168.098 170.844 1.01634
protein x 0001. [refseq;acc:nm_016302] Measured 6376.12 6833.59 1.07175
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Squared 27757.7 30828.3 1.11062
1583 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Ranked 168.091 170.837 1.01634
dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] Squared 15207.9 16886.9 1.1104
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Measured 6376.12 6833.59 1.07175
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Rooted 61.9705 64.1938 1.03588
1584 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Ranked 216.891 220.432 1.01633
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Measured 5933.25 6358.78 1.07172
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Squared 29259.9 32490 1.11039
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Rooted 61.9705 64.1938 1.03588
1585 26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6] Measured 5858.48 6278.32 1.07166
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Ranked 168.145 170.888 1.01631
growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Rooted 61.9703 64.1936 1.03588
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Squared 15537.9 17247.4 1.11002
1586 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] 26736.9 29677.3 1.10998
adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Ranked 222.166 225.79 1.01631
eyes absent homolog 4. [swissprot;acc:o95677] Rooted 61.9784 64.1991 1.03583
ubiquitin-like protein smt3c precursor (ubiquitin-homology domain protein pic1) (ubiquitin-like protein ubl1) (ubiquitin-related protein sumo-1) (gap modifying protein 1) (gmp1) (sentrin). [swissprot;acc:q93068] Measured 5784.36 6198.73 1.07164
1587 parafibromin. [refseq;acc:nm_024529] Squared 17179.4 19067.8 1.10992
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Ranked 220.129 216.598 1.0163
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Rooted 64.7716 67.0877 1.03576
udp-glucose 6-dehydrogenase (ec 1.1.1.22) (udp-glc dehydrogenase) (udp-glcdh) (udpgdh). [swissprot;acc:o60701] Measured 5784.36 6198.73 1.07164
1588 pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811] Rooted 61.9974 64.2136 1.03575
proteasome subunit beta type 5 precursor (ec 3.4.25.1) (proteasome epsilon chain) (macropain epsilon chain) (multicatalytic endopeptidase complex epsilon chain) (proteasome subunit x) (proteasome chain 6) (proteasome subunit mb1). [swissprot;acc:p28074] Squared 31589.1 35061.5 1.10992
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Ranked 177.834 180.725 1.01626
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Measured 3600.99 3360.33 1.07162
1589 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
eyes absent homolog 2. [swissprot;acc:o00167] Rooted 61.9889 64.2048 1.03575
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Squared 30900.2 34294.9 1.10986
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Ranked 223.589 227.219 1.01624
1590 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Squared 29261.2 32474.1 1.1098

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/