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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5541 to 5590 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1386 calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] Measured 6079.46 6555.41 1.07829
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Squared 19367.8 21747.4 1.12286
putative dimethylaniline monooxygenase [n-oxide forming] 6 (ec 1.14.13.8) (flavin-containing monooxygenase 6) (fmo 6) (dimethylaniline oxidase 6). [swissprot;acc:o60774] Rooted 60.9624 63.4098 1.04015
rho-gtpase activating protein 10. [refseq;acc:nm_020824] Ranked 218.47 213.876 1.02148
1387 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] Squared 19336.4 21711.3 1.12282
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Measured 6079.46 6555.4 1.07829
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Rooted 60.3917 62.8083 1.04002
sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Ranked 218.47 213.875 1.02148
1388 dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Rooted 60.9652 63.4052 1.04002
guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Squared 18314.2 20563 1.12279
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] Measured 5743.39 6192.94 1.07827
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Ranked 218.471 213.876 1.02148
1389 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] 218.47 213.875
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Rooted 93.3148 89.7311 1.03994
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Measured 6079.13 6554.85 1.07825
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Squared 18314.2 20563 1.12279
1390 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Ranked 218.47 213.875 1.02148
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Rooted 60.967 63.4023 1.03994
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Squared 50724.5 45178.9 1.12275
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Measured 5743.36 6192.72 1.07824
1391 dimethylaniline monooxygenase [n-oxide forming] 1 (ec 1.14.13.8) (fetal hepatic flavin-containing monooxygenase 1) (fmo 1) (dimethylaniline oxidase 1). [swissprot;acc:q01740] Rooted 60.9674 63.4016 1.03993
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Measured 5743.36 6192.7 1.07824
estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] Squared 26751.5 30026.4 1.12242
phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Ranked 218.47 213.875 1.02148
1392 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Rooted 93.2947 89.7137 1.03992
brachyury protein (t protein). [swissprot;acc:o15178] Squared 27044.4 30348.7 1.12218
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Ranked 218.471 213.876 1.02148
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] Measured 5743.36 6192.7 1.07824
1393 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 6192.72
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Rooted 60.968 63.4008 1.0399
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Ranked 218.47 213.875 1.02148
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Squared 27044.4 30348.7 1.12218
1394 alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] 23215.1 26051.5
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Ranked 218.47 213.875 1.02148
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Measured 5743.36 6192.72 1.07824
ubiquitin. [swissprot;acc:p02248] Rooted 68.9499 71.7002 1.03989
1395 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 65.478 68.0886 1.03987
beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] Squared 23215.1 26051.5 1.12218
growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Ranked 218.47 213.876 1.02148
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Measured 5743.26 6191.96 1.07813
1396 26s proteasome non-atpase regulatory subunit 6 (26s proteasome regulatory subunit s10) (p42a) (proteasome regulatory particle subunit p44s10). [swissprot;acc:q15008] Squared 27408.7 30747.3 1.12181
arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Rooted 69.8799 72.6645 1.03985
eyes absent homolog 1. [swissprot;acc:q99502] Ranked 218.463 213.872 1.02147
g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] Measured 5803.54 6256.54 1.07806
1397 40s ribosomal protein s8. [swissprot;acc:p09058] Ranked 218.64 214.049 1.02145
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Squared 50598.8 45106.3 1.12177
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597] Measured 5803.27 6256.23 1.07805
histone h4. [swissprot;acc:p02304] Rooted 60.8298 63.2514 1.03981
1398 calmegin precursor. [swissprot;acc:o14967] 62.3815 64.865
eyes absent homolog 4. [swissprot;acc:o95677] Ranked 218.449 213.864 1.02144

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/