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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 580 to 629 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
Network Comparison Type
red
green
network_comparison
73 Ranked kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Subtracted 265.632 319.531 53.899
Squared melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Divided 219048 129762 1.68808
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Subtracted 148058 99628.4 48429.6
Rooted deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 27.7078 44.017 16.3092
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided 27.9136 37.2872 1.33581
74 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 20446.1 24136.4 3690.3
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] Divided 4556.99 2945.8 1.54694
Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 288 362 1.25694
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] Subtracted 189.07 242.453 53.383
Squared a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 117858 70570.1 47287.9
trophinin. [swissprot;acc:q12816] Divided 219048 129762 1.68808
Rooted neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 27.9136 37.2872 1.33581
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Subtracted 27.7254 44.0299 16.3045
75 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 3690.3
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 1920.75 2907.43 1.5137
Ranked sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 288 362 1.25694
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Subtracted 254.693 202.668 52.025
Squared myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Divided 110342 184298 1.67024
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Subtracted 117850 70566.8 47283.2
Rooted chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Divided 27.9136 37.2872 1.33581
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Subtracted 27.7254 44.0299 16.3045
76 Measured homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 20446.1 24136.4 3690.3
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] Divided 4599.26 3058.57 1.50373
Ranked db83 protein. [swissprot;acc:p57088] 288 362 1.25694
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Subtracted 254.693 202.668 52.025
Squared cyclin g1 (cyclin g). [swissprot;acc:p51959] 117718 70505.8 47212.2
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Divided 110342 184298 1.67024
Rooted 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
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Subtracted 27.7254 44.0299 16.3045
77 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 20446.1 24136.4 3690.3
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] Divided 4612.39 3093.6 1.49095
Ranked voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 254.692 202.668 1.2567
Subtracted 52.024
Squared myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Divided 110342 184298 1.67024
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] Subtracted 117718 70505.9 47212.1
Rooted kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 27.7254 44.0299 16.3045
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Divided 39.9725 52.9973 1.32584
78 Measured cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 20446.1 24136.4 3690.3
Ranked voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 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
Squared 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
cyclin g2. [swissprot;acc:q16589] Subtracted 117718 70505.9 47212.1
Rooted nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 177.987 194.29 16.303
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Divided 63.7477 48.1589 1.3237
79 Measured homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 20446.1 24136.4 3690.3
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 3074.57 4567.51 1.48558
Ranked voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 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
Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Divided 117850 70566.8 1.67005

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/