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 1200 to 1249 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
150 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Measured Subtracted 4172.91 5954.48 1781.57
151 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Rooted Divided 38.8223 46.4975 1.1977
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Squared 250303 354894 1.41786
epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Subtracted 87971.9 69563.1 18408.8
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted 50.3065 62.9788 12.6723
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Ranked Divided 55 46 1.19565
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured Subtracted 14830.5 13050.3 1780.2
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked 226.582 198.444 28.138
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] Measured Divided 4578.09 5939.91 1.29746
152 high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 5136.78 6895.98 1759.2
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Rooted Divided 55.2859 65.9288 1.19251
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured 23693.7 18263 1.29736
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Ranked 55 46 1.19565
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Squared Subtracted 73995.1 56003.7 17991.4
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Divided 90226 126939 1.4069
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Ranked Subtracted 226.582 198.444 28.138
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Rooted 50.3247 62.9892 12.6645
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Ranked Divided 249.663 298.263 1.19466
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 226.582 198.444 28.138
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Measured Divided 23693.7 18263 1.29736
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted Subtracted 50.3333 62.9942 12.6609
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Divided 55.297 65.9236 1.19217
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Measured Subtracted 9035 7279.6 1755.4
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 17902.9
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Divided 70011 49783 1.40632
154 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Rooted 43.5479 51.5473 1.18369
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Subtracted 50.339 62.9975 12.6585
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Measured Divided 23693.7 18263 1.29736
musashi 2 isoform a. [refseq;acc:nm_138962] Ranked Subtracted 227.491 199.458 28.033
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Measured 9035 7279.6 1755.4
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Ranked Divided 249.663 298.263 1.19466
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Squared Subtracted 70525.9 52678.7 17847.2
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 42788.3 60162.6 1.40605
155 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 126408 89940.5 1.40546
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Subtracted 70525.9 52678.7 17847.2
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 66.7323 12.498
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured Divided 23693.7 18263 1.29736
musashi 1. [refseq;acc:nm_002442] Ranked Subtracted 227.491 199.458 28.033
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Measured 9035 7279.6 1755.4
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Ranked Divided 249.663 298.263 1.19466
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Rooted 55.7423 65.6839 1.17835
156 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Squared Subtracted 70525.9 52678.7 17847.2
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Rooted 55.1026 67.5701 12.4675
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured Divided 23693.7 18263 1.29736
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 9035 7279.6 1755.4
nuclear protein ukp68. [refseq;acc:nm_024824] Ranked 227.491 199.458 28.033
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Divided 249.663 298.263 1.19466
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 1.40528
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 1.17356
157 brain protein 44. [swissprot;acc:o95563] Squared 89182.8 125229 1.40418

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/