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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Gene Network Comparison Type Rank description Value Type red Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 6358 to 6407 of 25824 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
network_comparison
green
1590 fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Measured 6364.01 1.07155 6819.38
puromycin-sensitive aminopeptidase (ec 3.4.11.-) (psa). [swissprot;acc:p55786] Rooted 62.7026 1.03563 64.9366
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Ranked 225.119 1.01621 228.769
1591 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
leukotriene a-4 hydrolase (ec 3.3.2.6) (lta-4 hydrolase) (leukotriene a(4) hydrolase). [swissprot;acc:p09960] Rooted 62.7026 1.03563 64.9366
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Measured 6364.01 1.07155 6819.38
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Squared 29261.2 1.1098 32474.1
1592 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Measured 5853.1 1.07153 6271.79
dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] Rooted 62.7026 1.03563 64.9366
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Squared 29261.2 1.10979 32473.8
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Ranked 225.119 1.01621 228.769
1593 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] Squared 29261.2 1.10979 32473.8
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Measured 4977.77 1.07152 5333.78
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Rooted 60.0929 1.03561 62.2327
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Ranked 225.119 1.01621 228.769
1594 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 222.133 1.0162 225.731
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Squared 29261.2 1.10979 32473.8
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Rooted 64.5338 1.03556 66.8288
transportin-sr; importin 12. [refseq;acc:nm_012470] Measured 5184.94 1.07152 5555.76
1595 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Ranked 222.134 1.01619 225.731
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Rooted 55.3706 1.03556 57.3394
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Measured 6351.32 1.07149 6805.39
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Squared 17195.6 1.10964 19080.9
1596 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Ranked 222.134 1.01619 225.731
enigma protein; lim domain protein. [refseq;acc:nm_005451] Measured 5665.34 1.07148 6070.32
kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Rooted 55.3706 1.03556 57.3394
p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Squared 25787.8 1.10962 28614.7
1597 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Ranked 222.134 1.01619 225.731
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Measured 5665.34 1.07148 6070.32
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Squared 29261.6 1.10961 32468.9
mesoderm induction early response 1. [refseq;acc:nm_020948] Rooted 64.6178 1.03543 66.9075
1598 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Ranked 222.134 1.01619 225.731
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Measured 5068.17 1.07147 5430.41
myosin viia. [swissprot;acc:q13402] Squared 26326.2 1.1094 29206.2
proteasome subunit alpha type 3 (ec 3.4.25.1) (proteasome component c8) (macropain subunit c8) (multicatalytic endopeptidase complex subunit c8). [swissprot;acc:p25788] Rooted 64.6178 1.03543 66.9075
1599 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Measured 5184.45 1.07147 5554.97
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Ranked 217.871 1.01617 214.404
fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] Rooted 64.7608 1.03535 67.05
ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567] Squared 26326.2 1.1094 29206.2
1600 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Measured 6336.22 1.07145 6788.96
adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Ranked 222.103 1.01608 225.675
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Rooted 64.7842 1.0353 67.0713
ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459] Squared 26326.2 1.1094 29206.2
1601 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 29238.6 1.10929 32434.1
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Ranked 217.268 1.01602 213.842
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Measured 5232.14 1.07142 5605.8
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Rooted 68.186 1.0352 70.5859
1602 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] Squared 17081.4 1.10925 18947.6
dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] Rooted 61.8653 1.03515 64.0396
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Ranked 217.334 1.01599 213.914

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/