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 [...,...].
Gene Rank Value Type Filtered description red Interaction Map Network Comparison Type green network_comparison
Results: HTML CSV LaTeX Showing element 601 to 650 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Value Type
Filtered
description
red
green
network_comparison
76 Measured 0 dead-box protein. [refseq;acc:nm_018665] 313.667 183 1.71403
1 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] 4599.26 3058.57 1.50373
Ranked 0 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 3474 2695 1.28905
1 db83 protein. [swissprot;acc:p57088] 288 362 1.25694
Squared 0 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 20.3193 57.5264 2.83112
1 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 110342 184298 1.67024
Rooted 0 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 10.025 13.6105 1.35766
1 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] 27.9136 37.2872 1.33581
77 Measured 0 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 712.071 416.524 1.70956
1 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] 4612.39 3093.6 1.49095
Ranked 0 regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] 8821.32 11366.5 1.28853
1 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 254.692 202.668 1.2567
Squared 0 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 328.83 917.917 2.79146
1 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 110342 184298 1.67024
Rooted 0 tigger transposable element derived 6. [refseq;acc:nm_030953] 13.0605 17.6725 1.35313
1 sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 39.9725 52.9973 1.32584
78 Measured 0 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 161 95 1.69474
1 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
Ranked 0 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 7584.72 9706.12 1.27969
1 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 254.693 202.668 1.2567
Squared 0 transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 0.213018 0.591716 2.77777
1 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 117858 70570.1 1.67008
Rooted 0 tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 13.0525 17.6565 1.35273
1 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 63.7477 48.1589 1.3237
79 Measured 0 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 323.79 544.991 1.68316
1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 3074.57 4567.51 1.48558
Ranked 0 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 9465.55 12106.5 1.27901
1 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 254.693 202.668 1.2567
Squared 0 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 396.995 1088.19 2.74107
1 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 117850 70566.8 1.67005
Rooted 0 tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 13.0522 17.6559 1.35271
1 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] 63.7477 48.1588 1.3237
80 Measured 0 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 293 493 1.68259
1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 4133.47 5945.32 1.43834
Ranked 0 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 9102.34 11617.9 1.27636
1 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 254.691 202.668 1.25669
Squared 0 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 955.08 2589.83 2.71164
1 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] 117718 70505.9 1.66962
Rooted 0 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 44.2946 32.7593 1.35212
1 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] 63.7477 48.1594 1.32368
81 Measured 0 transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 30 50 1.66667
1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 4136.36 5943.56 1.43691
Ranked 0 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 14463 11356 1.2736
1 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 254.614 202.646 1.25645
Squared 0 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 45.9662 123.721 2.69156
1 cyclin g2. [swissprot;acc:q16589] 117718 70505.9 1.66962
Rooted 0 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 54.2583 40.2058 1.34951
1 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] 63.7475 48.1615 1.32362
82 Measured 0 importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 191.333 115.333 1.65896
1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 4172.91 5954.48 1.42694

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/