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 768 to 817 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
96 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Squared Subtracted 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
101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared Divided 222655 143584 1.5507
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 3225.65 1.3705
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted Subtracted 19.9625 35.798 15.8355
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Divided 47.6504 36.9304 1.29028
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Ranked 88.2482 110.265 1.24949
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted 204.641 161.051 43.59
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Measured 14924.4 17655.2 2730.8
septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 35900.4
102 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured 11068 8508.5 2559.5
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Rooted 19.9625 35.798 15.8355
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared Divided 214143 138337 1.54798
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Ranked Subtracted 204.642 161.068 43.574
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 88.2482 110.265 1.24949
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Squared Subtracted 121200 85473.4 35726.6
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Measured Divided 2353.63 3225.65 1.3705
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 36.9304 1.29028
103 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Measured 2353.63 3225.65 1.3705

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/