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 4308 to 4357 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
270 crk-like protein. [swissprot;acc:p46109] Rooted Divided 1 66.1064 74.1074 1.12103
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Ranked 0 10735.1 9891.37 1.0853
fad synthetase. [refseq;acc:nm_025207] 1 241.373 267.352 1.10763
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 1.21358
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Subtracted 0 157 56 101
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Squared 1 35508.6 44191.3 8682.7
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] 0 338.863 213.584 125.279
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Measured Divided 1217.96 1367.88 1.12309
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Rooted Subtracted 31.7744 33.8609 2.0865
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Measured 1 4810.22 6075.04 1264.82
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Rooted 48.0515 39.0445 9.007
transcription factor iib. [refseq;acc:nm_013242] Squared Divided 64739.9 50300.6 1.28706
zinc finger protein 277. [swissprot;acc:q9nrm2] Rooted 0 90.4079 98.9265 1.09422
271 60s ribosomal protein l39. [swissprot;acc:p02404] Measured Subtracted 3024.78 2923.92 100.86
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked Divided 1 241.373 267.352 1.10763
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 2554.89 3093.78 1.21092
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared Subtracted 53774.6 45105.5 8669.1
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Rooted 62.762 53.7761 8.9859
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Ranked 0 5781.93 6660.63 878.7
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Measured 1 4812.01 6076.09 1264.08
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared Divided 0 92.5367 74.2791 1.2458
histone h4. [swissprot;acc:p02304] Measured 21773.1 24446.3 1.12278
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Squared Subtracted 1872.12 1754.91 117.21
maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Rooted 25.5082 23.4377 2.0705
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Divided 17.4356 19.0526 1.09274
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Ranked 10735.1 9891.37 1.0853
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 1 243.072 266.559 23.487
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted Divided 66.1064 74.1073 1.12103
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared 64739.9 50300.6 1.28706
272 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 0 4225.7 5255.44 1.24369
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] Rooted Subtracted 21.9471 19.8816 2.0655
60s ribosomal protein l15. [swissprot;acc:p39030] Measured Divided 846.216 753.793 1.12261
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared 1 36563.7 46971.1 1.28464
chromodomain y-like protein 2. [refseq;acc:nm_152342] Rooted 0 33.0227 30.2263 1.09252
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 1 57.4432 66.3307 8.8875
fos-related antigen 2. [swissprot;acc:p15408] Ranked 0 7091.75 6217.28 874.47
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured Divided 1 3858.52 4669.27 1.21012
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 0 750.981 650.724 100.257
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked Divided 1 241.373 267.352 1.10763
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 266.248 23.418
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Measured 1991.03 3221.38 1230.35
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted Divided 66.1064 74.1074 1.12103
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared Subtracted 35247.5 43820.5 8573
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 240.689 124.83 115.859
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked Divided 7163.55 7759.61 1.08321
273 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Squared Subtracted 1 30826.5 39383.9 8557.4
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Divided 0 4224.07 5253.37 1.24367
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked 1 241.373 267.352 1.10763
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured Subtracted 0 658.544 758.411 99.867
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked 10432.4 11298.4 866

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/