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 630 to 679 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
79 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
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Ranked Divided 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 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 117515 70412.3 47102.7
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 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
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 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
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Ranked Divided 254.691 202.668 1.25669
81 cyclin g2. [swissprot;acc:q16589] Squared 117718 70505.9 1.66962
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted Subtracted 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
sedlin. [swissprot;acc:o14582] Squared Subtracted 112820 157033 44213
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 Divided 63.7475 48.1615 1.32362
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Ranked 254.614 202.646 1.25645
82 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Rooted 60.8022 79.5099 1.30768
cyclin g1 (cyclin g). [swissprot;acc:p51959] Squared 117718 70505.8 1.66962
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Ranked 267.636 335.359 1.25304
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted Subtracted 40.3337 24.2744 16.0593
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 3690.3
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 4172.91 5954.48 1.42694
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared Subtracted 112820 157033 44213
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked 252.329 202.004 50.325
83 bet3 homolog. [swissprot;acc:o43617] Squared 112820 157033 44213
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 40.3357 24.2915 16.0442
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 50.311
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 88.2482 110.265 1.24949
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Measured Subtracted 21644.2 18098.7 3545.5
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided 4932.27 7033.29 1.42597
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 117718 70505.9 1.66962
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] Rooted 63.6507 48.7127 1.30666
84 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 117515 70412.3 1.66896
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted Subtracted 40.3358 24.2919 16.0439
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Ranked Divided 88.2482 110.265 1.24949
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Subtracted 252.296 201.995 50.301
jun dimerization protein. [refseq;acc:nm_130469] Measured Divided 4932.27 7033.29 1.42597
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Rooted 46.7419 60.9337 1.30362
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared Subtracted 103496 146848 43352
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Measured 21632.5 18090 3542.5
85 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared Divided 67438.6 40697 1.65709
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Rooted 46.7419 60.9337 1.30362
fos-related antigen 2. [swissprot;acc:p15408] Measured 4941.95 7037.11 1.42395
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Rooted Subtracted 40.336 24.2941 16.0419
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Ranked Divided 88.2482 110.265 1.24949
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Squared Subtracted 103496 146848 43352
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Measured 21370.8 17896.5 3474.3

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/