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 Filtered network_comparison Interaction Map green red
Results: HTML CSV LaTeX Showing element 601 to 650 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
network_comparison
Interaction Map
green
red
76 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Rooted 1.33581 High confidence 37.2872 27.9136
db83 protein. [swissprot;acc:p57088] Ranked 1.25694 362 288
dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Rooted 1.09786 Low confidence 82.5511 75.1927
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 1.67024 High confidence 184298 110342
nipsnap1 protein. [swissprot;acc:q9bpw8] Ranked 1.10017 Low confidence 226.86 249.584
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Squared 1.23831 64605 52172
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured 1.11235 5933.4 5334.13
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 1.50373 High confidence 3058.57 4599.26
77 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Rooted 1.0978 Low confidence 75.4877 68.7629
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 1.11235 5933.4 5334.13
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared 1.67024 High confidence 184298 110342
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 1.23819 Low confidence 64594.5 52168.6
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Ranked 1.09994 215.424 195.851
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted 1.32584 High confidence 52.9973 39.9725
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Measured 1.49095 3093.6 4612.39
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Ranked 1.2567 202.668 254.692
78 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 1.67008 70570.1 117858
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured 1.48573 7132.71 4800.81
malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Ranked 1.0978 Low confidence 231.635 211
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Squared 1.23649 64447.1 52120.9
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 1.11235 5933.4 5334.13
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted 1.3237 High confidence 48.1589 63.7477
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Ranked 1.2567 202.668 254.693
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Rooted 1.0978 Low confidence 75.4877 68.7629
79 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Ranked 1.09742 208.803 229.144
cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Rooted 1.0978 75.4877 68.7629
ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Measured 1.11235 5933.4 5334.13
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1.48558 High confidence 4567.51 3074.57
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared 1.67005 70566.8 117850
rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872] 1.23446 Low confidence 228277 281799
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Rooted 1.3237 High confidence 48.1588 63.7477
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Ranked 1.2567 202.668 254.693
80 bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] Squared 1.23446 Low confidence 228277 281799
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Measured 1.43834 High confidence 5945.32 4133.47
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 1.11235 Low confidence 5933.4 5334.13
rad50-interacting protein 1. [refseq;acc:nm_021930] Ranked 1.09499 202.005 221.194
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Rooted 1.32368 High confidence 48.1594 63.7477
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Squared 1.66962 70505.9 117718
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Rooted 1.0978 Low confidence 75.4877 68.7629
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Ranked 1.25669 High confidence 202.668 254.691
81 cyclin g2. [swissprot;acc:q16589] Squared 1.66962 70505.9 117718
eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Rooted 1.0978 Low confidence 75.4877 68.7629
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured 1.43691 High confidence 5943.56 4136.36
regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] 1.11183 Low confidence 6146.97 5528.68
rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] Squared 1.23446 228277 281799
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Rooted 1.32362 High confidence 48.1615 63.7475
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 1.09286 Low confidence 208.281 227.623
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1.25645 High confidence 202.646 254.614
82 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Rooted 1.0978 Low confidence 75.4877 68.7629
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1.30768 High confidence 79.5099 60.8022

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/