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 1775 to 1824 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
222 proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured Subtracted 6417.18 7859.6 1442.42
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Squared Divided 86281 65058.3 1.32621
223 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 29567 18601.6 10965.4
cytohesin 4. [swissprot;acc:q9uia0] Measured Divided 41482.5 33356.5 1.24361
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted 137.446 120.823 1.13758
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Ranked 112 126 1.125
septin 6. [swissprot;acc:q14141] Rooted Subtracted 113.169 123.23 10.061
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 24.52
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Squared Divided 40982.6 54272.3 1.32428
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured Subtracted 6417.18 7859.59 1442.41
224 60s ribosomal protein l34. [swissprot;acc:p49207] Ranked 242.153 266.673 24.52
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Measured Divided 41482.5 33356.5 1.24361
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Rooted Subtracted 44.849 54.7964 9.9474
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 46021.4 56813.2 10791.8
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted Divided 137.446 120.823 1.13758
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked 185.969 165.623 1.12285
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured Subtracted 6417.18 7859.59 1442.41
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Squared Divided 14943.9 19771.9 1.32307
225 grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Measured Subtracted 6417.19 7859.51 1442.32
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted Divided 137.446 120.823 1.13758
metaxin 1. [swissprot;acc:q13505] Squared 60401.6 79875.7 1.32241
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Measured 9035 7279.6 1.24114
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared Subtracted 45986 56776.1 10790.1
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked 242.153 266.673 24.52
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided 226.471 201.769 1.12243
Rooted Subtracted 55.7423 65.6839 9.9416
226 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Ranked Divided 239.991 269.238 1.12187
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Measured Subtracted 6417.31 7858.12 1440.81
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Rooted Divided 137.446 120.823 1.13758
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Measured 9035 7279.6 1.24114
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Squared 73510.2 55607.3 1.32195
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked Subtracted 242.153 266.673 24.52
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Rooted 56.3447 66.124 9.7793
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared 45987 56777.1 10790.1
227 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 45985.9 56776
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Rooted 56.3507 66.1252 9.7745
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Measured 6417.33 7857.93 1440.6
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Rooted Divided 137.446 120.823 1.13758
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Ranked Subtracted 244.126 268.604 24.478
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Measured Divided 9035 7279.6 1.24114
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Squared 73995.1 56003.7 1.32125
thrombospondin 3 precursor. [swissprot;acc:p49746] Ranked 239.99 269.234 1.12186
228 band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Squared Subtracted 45986.7 56776.8 10790.1
enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Divided 57913.5 76336.3 1.31811
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 137.446 120.823 1.13758
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Ranked Subtracted 244.126 268.604 24.478
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted 95.0526 85.3206 9.732
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Measured Divided 9035 7279.6 1.24114
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Subtracted 6417.81 7852.52 1434.71
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Ranked Divided 226.411 202.088 1.12036

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.
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