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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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 1800 to 1849 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
225 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 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
229 60s ribosomal protein l3-like. [swissprot;acc:q92901] Subtracted 242.195 266.663 24.468
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Squared 45986 56776.1 10790.1
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked Divided 226.401 202.094 1.12028
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 1.13758
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Squared 42411.6 55802.1 1.31573
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted Subtracted 95.0526 85.3206 9.732
small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured 10434.4 11846.2 1411.8
230 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 10790.1
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Ranked Divided 239.35 267.915 1.11934
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Measured Subtracted 9649.61 11053.5 1403.89
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted Subtracted 95.0526 85.3206 9.732
necdin. [swissprot;acc:q99608] Divided 137.446 120.823 1.13758
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Ranked Subtracted 242.694 267.017 24.323
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared Divided 42411.6 55802.1 1.31573
231 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Subtracted 45960.8 56749.6 10788.8
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Ranked Divided 239.336 267.881 1.11927
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted 137.446 120.823 1.13758
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured 9035 7279.6 1.24114
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted Subtracted 95.0526 85.3206 9.732
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 226.411 202.088 24.323
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured 9649.61 11053.5 1403.89
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Squared Divided 42411.6 55802.1 1.31573
232 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked Subtracted 226.401 202.094 24.307

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/