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 3658 to 3707 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
915 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] Rooted 55.2209 52.1262 1.05937
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Squared 19364.5 22408.8 1.15721
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Ranked 146.036 140.692 1.03798
916 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Rooted 61.4775 65.1209 1.05926
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] Measured 6289.72 6911.96 1.09893
fibulin-1 precursor. [swissprot;acc:p23142] Squared 44407.1 51387.4 1.15719
hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] Ranked 232.512 241.288 1.03774
917 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Squared 23294.5 26946.3 1.15677
nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387] Measured 6289.72 6911.96 1.09893
parafibromin. [refseq;acc:nm_024529] Ranked 239.704 230.991 1.03772
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Rooted 82.3879 87.2663 1.05921
918 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 62.3496 66.0388 1.05917
metastasis-associated protein mta1. [swissprot;acc:q13330] Squared 23321.7 26976.4 1.15671
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Ranked 212.952 205.292 1.03731
scratch; scratch 1. [refseq;acc:nm_031309] Measured 7281.6 8001.64 1.09888
919 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Squared 23346.9 27004.3 1.15665
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Measured 5396.36 5929.41 1.09878
midasin (midas-containing protein). [swissprot;acc:q9nu22] Ranked 237.218 228.698 1.03725
p66 alpha. [refseq;acc:nm_017660] Rooted 93.8375 88.6044 1.05906
920 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Ranked 236.741 245.547 1.0372
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Measured 7273.78 7991.72 1.0987
protein cgi-147. [swissprot;acc:q9y3e5] Squared 36787.9 31806.3 1.15662
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Rooted 93.8375 88.6044 1.05906
921 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Squared 25739.7 29768.2 1.15651
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Ranked 236.741 245.547 1.0372
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Measured 6324.31 6948.5 1.0987
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Rooted 93.8375 88.6044 1.05906
922 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] Squared 27031.3 31257.4 1.15634
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Ranked 236.741 245.547 1.0372
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Measured 5511.2 6054.71 1.09862
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Rooted 62.0422 65.7019 1.05899
923 elongation factor 2 (ef-2). [swissprot;acc:p13639] Squared 23598.8 27286.9 1.15628
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Measured 4057.54 4457.66 1.09861
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Ranked 236.741 245.547 1.0372
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Rooted 62.0422 65.7019 1.05899
924 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Ranked 236.741 245.547 1.0372
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Squared 23598.8 27286.9 1.15628
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Measured 5406.5 5939.42 1.09857
925 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Rooted 62.0422 65.7019 1.05899
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Squared 23598.8 27286.9 1.15628
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Ranked 215.665 207.942 1.03714
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Measured 5637.43 6193.07 1.09856
926 cellular modulator of immune recognition. [refseq;acc:nm_145021] Rooted 62.0422 65.7019 1.05899
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Squared 17373.9 20087.4 1.15618
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Ranked 217.942 210.139 1.03713
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Measured 5637.45 6193.08 1.09856
927 dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] 5638.64 6194.22 1.09853
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Ranked 217.942 210.139 1.03713
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Squared 24049.1 27802.5 1.15607

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/