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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1082 to 1131 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
271 Ranked 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] 241.373 267.352 1.10763
Squared splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] 64739.9 50300.6 1.28706
Rooted proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] 66.1064 74.1073 1.12103
272 Measured histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 3858.52 4669.27 1.21012
Ranked ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 241.373 267.352 1.10763
Squared adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 36563.7 46971.1 1.28464
Rooted proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] 66.1064 74.1074 1.12103
273 Measured eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3199.4 3870.8 1.20985
Ranked 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] 241.373 267.352 1.10763
Squared filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 16120.1 20665.7 1.28198
Rooted proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] 66.1064 74.1074 1.12103
274 Measured chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 3119.98 2579.49 1.20953
Ranked nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] 241.373 267.352 1.10763
Squared rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 16120.1 20665.7 1.28198
Rooted 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] 66.1063 74.1068 1.12102
275 Measured regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 3119.98 2579.49 1.20953
Ranked cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] 241.373 267.352 1.10763
Squared protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 16120.1 20665.7 1.28198
Rooted ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 66.1048 74.0977 1.12091
276 Measured putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 3119.98 2579.49 1.20953
Ranked 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 266.969 1.10716
Squared protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 16120.1 20665.7 1.28198
Rooted homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 66.1046 74.0964 1.1209
277 Measured 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] 3119.98 2579.49 1.20953
Ranked 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 1.10665
Squared u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 16120.1 20665.7 1.28198
Rooted ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 65.9938 73.9449 1.12048
278 Measured transcription factor lbx1. [swissprot;acc:p52954] 3119.98 2579.49 1.20953
Ranked 40s ribosomal protein s11. [swissprot;acc:p04643] 241.399 267.088 1.10642
Squared filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 16120.1 20665.7 1.28198
Rooted ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 65.9938 73.9449 1.12048
279 Measured mosaic protein lgn. [swissprot;acc:p81274] 3119.98 2579.49 1.20953
Ranked histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 228.42 1.10605
Squared musashi 2 isoform a. [refseq;acc:nm_138962] 15569.5 19953.6 1.28158
Rooted neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 66.0989 74.0609 1.12046
280 Measured regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 3119.98 2579.49 1.20953
Ranked metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 1.10578
Squared musashi 1. [refseq;acc:nm_002442] 15569.5 19953.6 1.28158
Rooted ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 57.9068 64.8562 1.12001
281 Measured guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 3119.98 2579.49 1.20953
Ranked 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
Squared nuclear protein ukp68. [refseq;acc:nm_024824] 15569.5 19953.6 1.28158
Rooted u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 57.9068 64.8562 1.12001
282 Measured rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 3119.98 2579.49 1.20953
Ranked 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] 252.39 228.297 1.10553
Squared stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 59704 76460.4 1.28066
Rooted splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 57.9819 64.9302 1.11984
283 Measured polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 5221.28 6314.35 1.20935
Ranked 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
Squared deltex 2. [refseq;acc:nm_020892] 6627.24 8484.19 1.2802

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/