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 5658 to 5707 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
354 paraspeckle protein 1. [refseq;acc:nm_018282] Squared Divided 1 71360.3 57385.8 1.24352
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Ranked Subtracted 94 114 20
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Measured 6913.6 7907.05 993.45
syntaxin 10 (syn10). [swissprot;acc:o60499] Ranked Divided 234.691 257.442 1.09694
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Measured 12839 10911.1 1.17669
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 49.2848 54.5246 1.10632
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Squared Subtracted 0 35.0828 69.7867 34.7039
355 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 1 34129.6 40434.5 6304.9
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Rooted Divided 0 27.6061 28.9062 1.04709
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Ranked Subtracted 1 94 114 20
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Measured 4914.27 5907.12 992.85
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Rooted 0 9.36926 8.24639 1.12287
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 1 50.2801 43.4779 6.8022
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided 58.0752 64.23 1.10598
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 0 48 51 1.0625
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] Measured Subtracted 22878.7 22826.8 51.9
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Squared 16.2406 50.7408 34.5002
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 1 15588.1 19381.8 1.24337
syntaxin 6. [swissprot;acc:o43752] Ranked 234.673 257.414 1.09691
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Measured 12839 10911.1 1.17669
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Ranked Subtracted 0 8918.54 9465.32 546.78
356 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Squared 1 34129.6 40434.5 6304.9
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Ranked Divided 243.24 266.796 1.09684
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Rooted Subtracted 0 9.36926 8.24639 1.12287
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Squared 1282.67 1314.42 31.75
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Rooted Divided 37.0208 38.7581 1.04693
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] Measured Subtracted 22940.1 22888.8 51.3
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked Divided 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured 48 51 1.0625
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Ranked Subtracted 1 94 114 20
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Squared Divided 35247.5 43820.5 1.24322
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Ranked Subtracted 0 8918.54 9465.32 546.78
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Rooted Divided 1 58.0752 64.23 1.10598
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Measured 11004.2 12944.2 1.1763
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Subtracted 4914.27 5907.12 992.85
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 6.7971
357 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Divided 0 28.0711 26.8141 1.04688
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Squared Subtracted 1 34129.6 40434.5 6304.9
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Ranked Divided 243.12 266.661 1.09683
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] Measured Subtracted 0 22946.3 22895.1 51.2
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Ranked 10074 10609 535
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Rooted Divided 1 61.2684 67.755 1.10587
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 0 30.7569 31.8678 1.1109
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Measured Divided 1 5061.11 5950.22 1.17567
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 0 16321 15577 1.04776
Squared 0.545325 0.615621 1.12891
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Measured 48 51 1.0625

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/