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 2580 to 2629 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
323 heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Measured Subtracted 10247.8 11289 1041.2
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Squared 25326.3 18354.1 6972.2
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] Divided 33514.4 42370.8 1.26426
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Rooted Subtracted 125.493 117.944 7.549
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Measured Divided 4620.76 5501.94 1.1907
324 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Ranked Subtracted 242.238 264.11 21.872
40s ribosomal protein s23. [swissprot;acc:p39028] Divided 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
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Subtracted 25326.2 18354.1 6972.1
protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Measured 11773.7 10733.8 1039.9
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Rooted 125.447 117.906 7.541
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] Ranked Divided 243.944 268.195 1.09941
60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Subtracted 241.828 263.62 21.792
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 Divided 50.3803 45.4193 1.10923
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Measured Subtracted 8362.81 9402.7 1039.89
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 100.684 108.135 7.451
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Squared Divided 34506.3 43476 1.25994
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Subtracted 19321 12542.6 6778.4
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Divided 16177.9 19235.4 1.18899
326 40s ribosomal protein s16. [swissprot;acc:p17008] Ranked Subtracted 241.828 263.62 21.792
60s ribosomal protein l5. [swissprot;acc:p46777] Divided 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
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Squared Subtracted 19321 12542.6 6778.4
protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Measured 11773 10733.2 1039.8
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted 56.0466 63.4808 7.4342
327 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 21.785
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] Rooted Divided 50.3803 45.4193 1.10923
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
max protein. [swissprot;acc:p25912] Rooted Subtracted 56.3054 63.7148 7.4094
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Squared 19321 12542.6 6778.4
peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284] Measured 11773 10733.2 1039.8
septin 10 isoform 1. [refseq;acc:nm_144710] Divided 16067.4 19094.4 1.18839
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Ranked 258.437 235.183 1.09888
brain protein 44. [swissprot;acc:o95563] Measured 15999.1 19007.1 1.18801
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Squared 16442.8 20662.7 1.25664
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 19321 12542.6 6778.4
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Rooted Divided 50.3803 45.4193 1.10923
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Ranked Subtracted 240.801 262.34 21.539
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Rooted 124.41 117.043 7.367
udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294] Measured 11773 10733.2 1039.8
329 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Rooted Divided 50.3803 45.4193 1.10923
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] Measured Subtracted 11773 10733.2 1039.8
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Ranked 191.644 170.192 21.452
metaxin 2. [swissprot;acc:o75431] Squared Divided 41236 51807 1.25635
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 19321 12542.6 6778.4

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/