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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2610 to 2659 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
164 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Measured Divided 0 1711.55 1354.26 1.26383
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked Subtracted 1 133 105 28
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared Divided 0 145.887 91.0551 1.60218
deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted 1 61733.5 45224.1 16509.4
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] Ranked Divided 0 11971.7 10412.4 1.14975
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Squared Subtracted 14421.3 14982.3 561
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Divided 1 173408 242989 1.40126
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Ranked 209.299 249.187 1.19058
mad protein (max dimerizer). [swissprot;acc:q05195] Rooted 55.646 65.1534 1.17086
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Measured 23693.7 18263 1.29736
musashi 2 isoform a. [refseq;acc:nm_138962] Rooted Subtracted 54.9787 66.2416 11.2629
neurocalcin delta. [swissprot;acc:p29554] Ranked 0 13973.6 15473.5 1499.9
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Measured 1475.83 1676.18 200.35
Rooted 22.1344 25.2414 3.107
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Divided 17.1341 14.7892 1.15855
165 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] Ranked Subtracted 8375.43 9873.58 1498.15
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Divided 1 209.299 249.187 1.19058
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Measured Subtracted 4489.19 2765.82 1723.37
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared Divided 173408 242989 1.40126
integral membrane protein cii-3b. [sptrembl;acc:o75609] Subtracted 0 15669.3 16209.3 540
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Rooted Divided 1 55.6486 65.1478 1.1707
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Measured 23693.7 18263 1.29736
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 0 1002.2 793.818 1.26251
musashi 1. [refseq;acc:nm_002442] Rooted Subtracted 1 54.9787 66.2416 11.2629
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared Divided 0 54383.4 34012.2 1.59894
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Measured Subtracted 293 493 200
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] Ranked Divided 13255.4 15183.2 1.14544
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Rooted Subtracted 26.1597 29.2445 3.0848
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 1 133 105 28
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Squared 59016.1 75486.9 16470.8
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Rooted Divided 0 17.1346 14.7899 1.15853
166 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared Subtracted 1 69201.8 53013.4 16188.4
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured Divided 0 5629.62 7099.51 1.2611
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Ranked Subtracted 14554.5 16027.9 1473.4
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Divided 1 209.299 249.187 1.19058
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured Subtracted 4489.19 2765.82 1723.37
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Squared Divided 173408 242989 1.40126
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 0 220.039 350.57 1.59322
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Rooted 1 55.6495 65.1458 1.17064
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Measured 23693.7 18263 1.29736
mesoderm induction early response 1. [refseq;acc:nm_020948] Rooted Subtracted 0 43.1585 40.0869 3.0716
my016 protein. [sptrembl;acc:q9h3k6] Ranked Divided 5561.19 6366.91 1.14488
neurocalcin delta. [swissprot;acc:p29554] Squared Subtracted 4946.59 5466.65 520.06
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked 1 312 284 28
nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 54.9787 66.2416 11.2629
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided 0 17.1395 14.7969 1.15832
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Measured Subtracted 320.012 120.429 199.583
167 60s ribosomal protein l15. [swissprot;acc:p39030] Ranked 11745.2 13203.1 1457.9
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 1 133 105 28
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared 64975.9 81151.2 16175.3

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/