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 1258 to 1307 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
315 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Rooted 95.0526 85.3206 1.11406
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Squared 71576.8 56326.7 1.27074
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured 21370.8 17896.5 1.19413
316 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Rooted 95.0526 85.3206 1.11406
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Squared 28918.3 36746 1.27068
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked 242.694 267.017 1.10022
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Measured 21370.8 17896.5 1.19413
317 adiponectin receptor 2. [refseq;acc:nm_024551] 3153.1 3762.56 1.19329
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Rooted 95.0526 85.3206 1.11406
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Squared 33982.3 43159.1 1.27005
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Ranked 224.445 204.044 1.09998
318 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 242.011 266.18 1.09987
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Squared 46739.9 59134.5 1.26518
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Rooted 95.0526 85.3206 1.11406
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Measured 34190.9 40795.8 1.19318
319 60s ribosomal protein l19. [swissprot;acc:p14118] Ranked 240.73 264.729 1.09969
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Squared 46739.9 59134.5 1.26518
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured 20911 24908.5 1.19117
saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] Rooted 49.0663 54.4978 1.1107
320 40s ribosomal protein s29. [swissprot;acc:p30054] 50.2784 45.294 1.11005
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Ranked 241.892 265.96 1.0995
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Squared 87971.9 69563.1 1.26463
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured 20911 24908.5 1.19117
321 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked 241.892 265.959 1.09949
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared 33526 42390.2 1.2644
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Measured 20911 24908.5 1.19117
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted 55.9231 62.0565 1.10968
322 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Measured 20911 24908.5 1.19117
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Ranked 86.7483 78.8995 1.09948
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Squared 33522.8 42384.8 1.26436
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted 60.594 67.2244 1.10942
323 60s ribosomal protein l23a. [swissprot;acc:p29316] Ranked 241.884 265.945 1.09947
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Rooted 50.3803 45.4193 1.10923
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Squared 33514.4 42370.8 1.26426
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured 4620.76 5501.94 1.1907
324 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked 243.944 268.195 1.09941
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Measured 28136.5 33457.6 1.18912
fad synthetase. [refseq;acc:nm_025207] Rooted 50.3803 45.4193 1.10923
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] Squared 34527.9 43507.9 1.26008
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked 243.944 268.195 1.09941
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Rooted 50.3803 45.4193 1.10923
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared 34506.3 43476 1.25994
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured 16177.9 19235.4 1.18899
326 60s ribosomal protein l5. [swissprot;acc:p46777] Ranked 241.899 265.924 1.09932
anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Squared 69124.3 54897.4 1.25915
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Measured 3432.96 4081.21 1.18883
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Rooted 50.3803 45.4193 1.10923
327 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252]
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Ranked 243.817 267.962 1.09903
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Squared 16424.1 20645.8 1.25704

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/