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 3682 to 3731 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
921 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
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Rooted 62.0422 65.7019 1.05899
928 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] Measured 5638.46 6194.04 1.09853
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Rooted 62.0422 65.7019 1.05899
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Ranked 225.976 218.017 1.03651
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Squared 20685.1 23904.8 1.15565
929 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Ranked 225.955 218.015 1.03642
surfeit locus protein 1. [swissprot;acc:q15526] Measured 5638.46 6194.04 1.09853
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Squared 22626.3 26143 1.15543
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Rooted 62.3617 66.0327 1.05887
930 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Measured 5638.65 6194.23 1.09853
homolog of yeast maf1. [refseq;acc:nm_032272] Squared 26029.5 30074.5 1.1554
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Ranked 231.357 239.778 1.0364
931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13 164.917 1.03637
sec13-related protein. [swissprot;acc:p55735] Rooted 62.3618 66.0328 1.05887
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Measured 5638.59 6194.17 1.09853
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Squared 26029.5 30074.5 1.1554
932 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Measured 5638.46 6194.04 1.09853
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] Ranked 225.939 218.013 1.03636
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Squared 26029.5 30074.5 1.1554
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Rooted 62.3617 66.0327 1.05887
933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Ranked 159.165 164.951 1.03635
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Measured 5638.46 6194.04 1.09853
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Squared 26029.5 30074.5 1.1554

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/