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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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 1244 to 1293 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
78 transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Squared Divided 0 0.213018 0.591716 2.77777
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Rooted Subtracted 48.2208 42.3517 5.8691
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Divided 1 63.7477 48.1589 1.3237
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Ranked Subtracted 254.691 202.668 52.023
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Divided 254.693 1.2567
79 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Measured Subtracted 0 2464 2076.5 387.5
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 1 20446.1 24136.4 3690.3
neuralized-like. [refseq;acc:nm_004210] Rooted 27.9107 44.1656 16.2549
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Ranked Divided 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
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Subtracted 8335.79 6506.81 1828.98
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Measured Divided 323.79 544.991 1.68316
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 3074.57 4567.51 1.48558
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Rooted Subtracted 0 43.2078 37.3703 5.8375
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Squared Divided 1 117850 70566.8 1.67005
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Ranked Subtracted 0 8821.32 11366.5 2545.18
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 Divided 1 63.7477 48.1588 1.3237
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Squared Subtracted 117718 70505.9 47212.1
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Rooted Divided 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
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Subtracted 254.614 202.646 51.968
80 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] Rooted Divided 0 44.2946 32.7593 1.35212
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Squared Subtracted 1 117515 70412.3 47102.7
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Rooted 0 105.939 111.683 5.744
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Ranked Divided 9102.34 11617.9 1.27636
Subtracted 2515.56
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 1 20446.1 24136.4 3690.3
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Divided 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
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Subtracted 7071.05 5421.2 1649.85
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 Divided 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
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Ranked Subtracted 294.053 242.562 51.491
transcription factor jun-b. [swissprot;acc:p17275] Rooted 63.4173 79.5311 16.1138
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] Measured 0 2464 2076.5 387.5
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Ranked Divided 1 254.691 202.668 1.25669
81 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Subtracted 0 7704.7 10174.1 2469.4
cyclin g2. [swissprot;acc:q16589] Squared Divided 1 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
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 40.3337 24.2744 16.0593
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 20446.1 24136.4 3690.3
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Ranked 252.371 202.016 50.355
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Measured Divided 4136.36 5943.56 1.43691
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Subtracted 0 2715.75 3103.01 387.26
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Squared Divided 45.9662 123.721 2.69156
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Subtracted 8755.38 7114.89 1640.49
sedlin. [swissprot;acc:o14582] 1 112820 157033 44213
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked Divided 0 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

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/