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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1213 to 1262 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
304 no value Ranked 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 266.986 1.1017
ABL1 Squared proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 28896.2 36767 1.27238
PRPF31 Measured pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 4855.46 5824.52 1.19958
PSCD4 Rooted cytohesin 4. [swissprot;acc:q9uia0] 203.673 182.638 1.11517
305 FYN Squared proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 28896.2 36767 1.27238
MRPL2 Ranked mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] 242.339 266.986 1.1017
OSR1 Measured odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 3856.29 4624.15 1.19912
PSCD3 Rooted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 203.673 182.638 1.11517
306 no value Measured pnas-18. [sptrembl;acc:q9bzu3] 13680.5 11409.6 1.19903
Ranked 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 266.673 1.10126
FGR Squared proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 28896.2 36767 1.27238
RBM39 Rooted rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] 56.3935 62.8817 1.11505
307 CCT3 Measured t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 12365.2 14824.9 1.19892
GRAP2 Squared 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] 28896.4 36766.8 1.27237
SIN3A Rooted transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 50.4687 45.2733 1.11476
SRR Ranked serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] 242.153 266.673 1.10126
308 AGPAT3 Squared 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] 30596.2 38919.9 1.27205
DENR Rooted density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 50.4687 45.2733 1.11476
DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 4977.09 5966.44 1.19878
RPL34 Ranked 60s ribosomal protein l34. [swissprot;acc:p49207] 242.153 266.673 1.10126
309 no value Rooted u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 56.185 62.6036 1.11424
CUTL1 Squared ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 28900.8 36762.6 1.27203
DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 4977.8 5966.14 1.19855
SEC61A2 Ranked protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] 242.153 266.673 1.10126
310 no value Rooted myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 95.0526 85.3206 1.11406
CUTL2 Squared homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 28901.4 36762.1 1.27198
SART1 Measured 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] 4909.79 5878.79 1.19736
SEC61A1 Ranked protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] 242.153 266.673 1.10126
311 AGPAT4 Squared 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] 30566.4 38866.5 1.27154
DVL3 Measured segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 4981.52 5964.58 1.19734
EIF1B Ranked protein translation factor sui1 homolog gc20. [swissprot;acc:o60739] 242.627 267.151 1.10108
MYH4 Rooted myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 95.0526 85.3206 1.11406
312 no value Measured u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 4598.21 5500.48 1.19622
Squared methyltransferase like 2. [refseq;acc:nm_018396] 71576.8 56326.7 1.27074
MYH8 Rooted myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 95.0526 85.3206 1.11406
RPL3L Ranked 60s ribosomal protein l3-like. [swissprot;acc:q92901] 242.195 266.663 1.10103
313 DYNLT1 Squared cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] 71576.8 56326.7 1.27074
MYH2 Rooted myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 95.0526 85.3206 1.11406
PPP1R2 Measured protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 21644.2 18098.7 1.1959
RRM2B Ranked ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 232.473 211.207 1.10069
314 FZR1 Squared fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 71576.8 56326.7 1.27074
METAP1 Ranked methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] 244.126 268.604 1.10027
MYH3 Rooted myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 95.0526 85.3206 1.11406
PPP1R2P9 Measured type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 21632.5 18090 1.19583
315 METAP2 Ranked 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] 244.126 268.604 1.10027
MYH1 Rooted myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 95.0526 85.3206 1.11406
PCSK5 Squared proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] 71576.8 56326.7 1.27074
RRS1 Measured ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] 21370.8 17896.5 1.19413
316 no value Rooted myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 95.0526 85.3206 1.11406
EIF1 Ranked protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 242.694 267.017 1.10022

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
- Hugo is the HGNC identifier if it exists
- 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/