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 663 to 712 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
332 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 0 15411.3 14167 1.08783
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 1 5051.16 5975.51 1.183
333 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 0 634.305 584.237 1.0857
334 peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 3161.12 2924.8 1.0808
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 1 14924.4 17655.2 1.18298
335 germ cell-less. [refseq;acc:nm_022471] 0 1829.81 1694.05 1.08014
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 1 3494.31 4129.6 1.18181
336 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 0 1766.66 1908.13 1.08008
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 1 3751.3 4431.34 1.18128
337 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 0 2039.07 2194.52 1.07624
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 1 20446.1 24136.4 1.18049
338 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]
lamin b2. [swissprot;acc:q03252] 0 579.262 538.704 1.07529
339 glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] 996.883 1070.03 1.07338
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 1 20446.1 24136.4 1.18049
340 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 0 559.333 600 1.07271
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1 20446.1 24136.4 1.18049
341 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 0 6452.66 6019.79 1.07191
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 1 20446.1 24136.4 1.18049
342 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 0 3691.15 3952.59 1.07083
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 1 20446.1 24136.4 1.18049
343 bystin. [swissprot;acc:q13895] 0 2930.88 3135.76 1.0699
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 1 20446.1 24136.4 1.18049
344 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 0 2075.64 2220.68 1.06988
345 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 2113.27 2255.28 1.0672
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 1 20446.1 24136.4 1.18049
346 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 0 1837.26 1721.76 1.06708
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 1 14229.2 16780.7 1.17931
347 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 0 1491.75 1591.6 1.06693
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 1 4991.02 5885.09 1.17914
348 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 0 14357.1 13463.1 1.0664
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 1 4991.02 5885.09 1.17914
349 kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 0 957.833 898.833 1.06564
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 1 4714.85 5554.38 1.17806
350 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 0 48 51 1.0625
sedlin. [swissprot;acc:o14582] 1 17396.9 20483.9 1.17745
351 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 0 48 51 1.0625
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 1 17396.9 20483.9 1.17745
352 bet3 homolog. [swissprot;acc:o43617]
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 0 48 51 1.0625
353 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
p66 alpha. [refseq;acc:nm_017660] 1 12839 10911.1 1.17669
354 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 0 48 51 1.0625
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 1 12839 10911.1 1.17669
355 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 0 48 51 1.0625
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 1 12839 10911.1 1.17669
356 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 0 48 51 1.0625
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 1 11004.2 12944.2 1.1763

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/