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 1208 to 1257 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
302 tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared 28896.2 36767 1.27238
303 60s ribosomal protein l35. [swissprot;acc:p42766] Ranked 242.333 266.999 1.10179
crk-like protein. [swissprot;acc:p46109] Squared 28896.2 36767 1.27238
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 182.638 1.11517
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured 22268.8 18560.4 1.1998
304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked 242.339 266.986 1.1017
cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 1.11517
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Measured 4855.46 5824.52 1.19958
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared 28896.2 36767 1.27238
305 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted 203.673 182.638 1.11517
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Ranked 242.339 266.986 1.1017
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Measured 3856.29 4624.15 1.19912
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 28896.2 36767 1.27238
306 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Ranked 242.153 266.673 1.10126
pnas-18. [sptrembl;acc:q9bzu3] Measured 13680.5 11409.6 1.19903
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared 28896.2 36767 1.27238
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Rooted 56.3935 62.8817 1.11505
307 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] Squared 28896.4 36766.8 1.27237
serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Ranked 242.153 266.673 1.10126
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured 12365.2 14824.9 1.19892
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Rooted 50.4687 45.2733 1.11476
308 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Squared 30596.2 38919.9 1.27205
60s ribosomal protein l34. [swissprot;acc:p49207] Ranked 242.153 266.673 1.10126
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Rooted 50.4687 45.2733 1.11476
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Measured 4977.09 5966.44 1.19878
309 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Squared 28900.8 36762.6 1.27203
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Ranked 242.153 266.673 1.10126
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured 4977.8 5966.14 1.19855
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Rooted 56.185 62.6036 1.11424
310 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Squared 28901.4 36762.1 1.27198
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Rooted 95.0526 85.3206 1.11406
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Ranked 242.153 266.673 1.10126
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Measured 4909.79 5878.79 1.19736
311 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Squared 30566.4 38866.5 1.27154
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Rooted 95.0526 85.3206 1.11406
protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] Ranked 242.627 267.151 1.10108
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured 4981.52 5964.58 1.19734
312 60s ribosomal protein l3-like. [swissprot;acc:q92901] Ranked 242.195 266.663 1.10103
methyltransferase like 2. [refseq;acc:nm_018396] Squared 71576.8 56326.7 1.27074
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Rooted 95.0526 85.3206 1.11406
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Measured 4598.21 5500.48 1.19622
313 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 71576.8 56326.7 1.27074
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Rooted 95.0526 85.3206 1.11406
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured 21644.2 18098.7 1.1959
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked 232.473 211.207 1.10069
314 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 1.27074
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Ranked 244.126 268.604 1.10027
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Rooted 95.0526 85.3206 1.11406
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Measured 21632.5 18090 1.19583
315 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 244.126 268.604 1.10027

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/