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 3508 to 3557 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
220 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Measured Subtracted 0 326.677 472.605 145.928
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Divided 1 41482.5 33356.5 1.24361
metastasis-associated protein mta1. [swissprot;acc:q13330] Rooted 52.7557 60.035 1.13798
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Ranked Subtracted 242.339 266.986 24.647
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 112 126 1.125
neurocalcin delta. [swissprot;acc:p29554] 0 13973.6 15473.5 1.10734
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] Subtracted 5677.58 4549.85 1127.73
pnas-18. [sptrembl;acc:q9bzu3] Rooted 24.2086 21.6857 2.5229
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Divided 24.1656 21.3198 1.13348
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Squared Subtracted 952.068 697.024 255.044
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Divided 19892.6 27221.2 1.36841
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured 18704 21730 1.16178
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared Subtracted 1 57808.9 46630.3 11178.6
221 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 0 1742.44 1500.84 241.6
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] Divided 1614.86 1181.19 1.36715
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Measured 1 41482.5 33356.5 1.24361
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Ranked 0 12190.3 13497.2 1.10721
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Subtracted 5677.45 4550.87 1126.58
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared Divided 1 70739 93908.8 1.32754
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Measured Subtracted 0 1225.09 1079.36 145.73
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Ranked Divided 1 112 126 1.125
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Subtracted 242.627 267.151 24.524
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 6417.18 7859.6 1442.42
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Divided 0 1905.84 1643 1.15998
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Rooted Subtracted 1 113.374 123.463 10.089
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 0 42.9302 40.4104 2.5198
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Divided 1 56.9506 64.7888 1.13763
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared Subtracted 57579.2 46497.2 11082
tubby protein homolog. [swissprot;acc:p50607] Rooted Divided 0 39.7788 45.0452 1.13239
222 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked 12183 11013.2 1.10622
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Measured 1499.4 1735.23 1.15728
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked Subtracted 1 242.153 266.673 24.52
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Rooted Divided 52.7936 60.0592 1.13762
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Squared 0 410.662 561.35 1.36694
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Measured 1 41482.5 33356.5 1.24361
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Ranked 112 126 1.125
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Rooted Subtracted 0 23.5797 26.096 2.5163
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Measured 1225.09 1079.36 145.73
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted 1 61.6639 71.7355 10.0716
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 29570.7 18601.8 10968.9
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Measured 6417.18 7859.6 1442.42
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 0 5673.33 6797.56 1124.23
Rooted Divided 58.6947 51.8401 1.13223
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Squared 1 86281 65058.3 1.32621
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Subtracted 0 1742.44 1500.84 241.6
223 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 374.181 141.849 232.332
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 1 29567 18601.6 10965.4
brain protein 16. [refseq;acc:nm_016458] Rooted Divided 0 38.9679 44.0549 1.13054
cytohesin 4. [swissprot;acc:q9uia0] Measured 1 41482.5 33356.5 1.24361
dc11 protein. [refseq;acc:nm_020186] Rooted Subtracted 0 23.5797 26.096 2.5163

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/