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 Filtered Network Comparison Type Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 601 to 650 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
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 27.9136 37.2872 1.33581
db83 protein. [swissprot;acc:p57088] Ranked 288 362 1.25694
dead-box protein. [refseq;acc:nm_018665] Measured 0 313.667 183 1.71403
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Squared 1 110342 184298 1.67024
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 20.3193 57.5264 2.83112
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] Measured 1 4599.26 3058.57 1.50373
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Ranked 0 3474 2695 1.28905
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Rooted 10.025 13.6105 1.35766
77 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Squared 328.83 917.917 2.79146
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Measured 712.071 416.524 1.70956
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared 1 110342 184298 1.67024
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Ranked 0 8821.32 11366.5 1.28853
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted 1 39.9725 52.9973 1.32584
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 4612.39 3093.6 1.49095
tigger transposable element derived 6. [refseq;acc:nm_030953] Rooted 0 13.0605 17.6725 1.35313
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Ranked 1 254.692 202.668 1.2567
78 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared 117858 70570.1 1.67008
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured 4800.81 7132.71 1.48573
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 0 161 95 1.69474
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Ranked 7584.72 9706.12 1.27969
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Rooted 13.0525 17.6565 1.35273
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Squared 0.213018 0.591716 2.77777
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted 1 63.7477 48.1589 1.3237
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Ranked 254.693 202.668 1.2567
79 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 0 9465.55 12106.5 1.27901
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Squared 396.995 1088.19 2.74107
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Measured 323.79 544.991 1.68316
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 3074.57 4567.51 1.48558
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared 117850 70566.8 1.67005
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 63.7477 48.1588 1.3237
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 0 13.0522 17.6559 1.35271
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Ranked 1 254.693 202.668 1.2567
80 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Rooted 0 44.2946 32.7593 1.35212
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked 9102.34 11617.9 1.27636
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Measured 1 4133.47 5945.32 1.43834
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 293 493 1.68259
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Squared 955.08 2589.83 2.71164
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 63.7477 48.1594 1.32368
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 117718 70505.9 1.66962
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Ranked 254.691 202.668 1.25669
81 cyclin g2. [swissprot;acc:q16589] Squared 117718 70505.9 1.66962
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Rooted 0 54.2583 40.2058 1.34951
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured 1 4136.36 5943.56 1.43691
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Squared 0 45.9662 123.721 2.69156
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked 14463 11356 1.2736
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 63.7475 48.1615 1.32362
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Measured 0 30 50 1.66667
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Ranked 1 254.614 202.646 1.25645
82 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Squared 0 374.181 141.849 2.63788
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted 1 60.8022 79.5099 1.30768

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/