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 751 to 800 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
94 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared Divided 84857.8 53402.4 1.58903
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Measured Subtracted 17396.9 20483.9 3087
95 bet3 homolog. [swissprot;acc:o43617]
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Rooted 40.2804 24.3692 15.9112
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked Divided 88.2482 110.265 1.24949
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared 256169 162517 1.57626
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Ranked Subtracted 249.663 298.263 48.6
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted Divided 47.6504 36.9304 1.29028
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] Measured 2397.19 3343.62 1.39481
tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared Subtracted 123324 86277.9 37046.1
96 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Divided 7744.68 4959.41 1.56161
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Ranked Subtracted 201.949 153.671 48.278
guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] Rooted 40.28 24.37 15.91
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Divided 4110.14 5694.99 1.3856
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Ranked 88.2482 110.265 1.24949
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Rooted 47.6504 36.9304 1.29028
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Subtracted 16177.9 19235.4 3057.5
Squared 90226 126939 36713
97 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Measured Divided 2820.51 3897.1 1.3817
Ranked Subtracted 271.752 225.68 46.072
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Squared Divided 227160 146079 1.55505
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Subtracted 126408 89940.5 36467.5
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Rooted 40.2797 24.3705 15.9092
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked Divided 88.2482 110.265 1.24949
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Rooted 47.6504 36.9304 1.29028
septin 10 isoform 1. [refseq;acc:nm_144710] Measured Subtracted 16067.4 19094.4 3027
98 brain protein 44. [swissprot;acc:o95563] 15999.1 19007.1 3008
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Rooted 40.2797 24.3705 15.9092
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked Divided 88.2482 110.265 1.24949
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Measured 2353.63 3225.65 1.3705
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Ranked Subtracted 204.641 160.957 43.684
septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 36304.3
transcription factor lbx1. [swissprot;acc:p52954] Rooted Divided 47.6504 36.9304 1.29028
trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 146079 1.55505
99 brain protein 44. [swissprot;acc:o95563] Subtracted 89182.8 125229 36046.2
jun dimerization protein. [refseq;acc:nm_130469] Ranked 204.641 160.957 43.684
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Rooted 47.6504 36.9304 1.29028
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Measured 2353.63 3225.65 1.3705
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 15999.1 19007.1 3008
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Rooted 19.9625 35.798 15.8355
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared Divided 226186 145568 1.55382
100 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Measured 2353.63 3225.65 1.3705
fos-related antigen 2. [swissprot;acc:p15408] Ranked Subtracted 204.641 161.046 43.595
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 36.9304 1.29028
septin 6. [swissprot;acc:q14141] Measured Subtracted 15959.9 18957.1 2997.2
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared 89182.8 125229 36046.2
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Rooted 19.9625 35.798 15.8355

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/