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 2558 to 2607 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
320 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Ranked Subtracted 88.2482 110.265 22.0168
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Measured Divided 20911 24908.5 1.19117
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Subtracted 10263.8 11318.6 1054.8
321 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Ranked Divided 241.892 265.959 1.09949
fibulin-1 precursor. [swissprot;acc:p23142] Squared Subtracted 44407.1 51387.4 6980.3
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Rooted 77.58 70.0181 7.5619
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Squared Divided 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
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Subtracted 11797.1 10750.2 1046.9
trophinin. [swissprot;acc:q12816] Ranked 88.2482 110.265 22.0168
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Rooted Divided 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
carboxypeptidase b precursor. [refseq;acc:nm_020361] Squared Subtracted 25326.4 18354.1 6972.3
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Ranked Divided 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
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Rooted Subtracted 77.5797 70.0179 7.5618
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Measured 9304.83 10347.3 1042.47
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted Divided 60.594 67.2244 1.10942
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Ranked Subtracted 231.969 210.064 21.905
323 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 242.238 264.11 21.872
60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 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
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

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/