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 Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1218 to 1267 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
77 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Squared Divided 0 328.83 917.917 2.79146
heat shock factor binding protein 1. [swissprot;acc:o75506] Measured Subtracted 1631.18 1233.41 397.77
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 1 20446.1 24136.4 3690.3
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Divided 0 712.071 416.524 1.70956
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted Subtracted 1 27.7254 44.0299 16.3045
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Squared Divided 110342 184298 1.67024
nanos (fragment). [sptrembl;acc:q8wy41] Ranked Subtracted 0 8782 11350 2568
p28 ing5. [refseq;acc:nm_032329] Squared 5071.93 3165.6 1906.33
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Ranked Divided 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, 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 Subtracted 117718 70505.9 47212.1
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] Measured Divided 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
Subtracted 52.024
78 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Squared Divided 117858 70570.1 1.67008
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Subtracted 0 71297.2 69420.1 1877.1
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured Divided 1 4800.81 7132.71 1.48573
cyclin g2. [swissprot;acc:q16589] Squared Subtracted 117718 70505.9 47212.1
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Ranked 0 7853.67 10406.3 2552.63
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured 1 20446.1 24136.4 3690.3
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Divided 0 161 95 1.69474
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Rooted Subtracted 1 177.987 194.29 16.303
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Ranked Divided 0 7584.72 9706.12 1.27969
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Measured Subtracted 1251.66 858.525 393.135
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Rooted Divided 13.0525 17.6565 1.35273
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Squared 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

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/