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.


Navigation/Query Panel:
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 [...,...].
Gene Rank description Value Type Network Comparison Type red Interaction Map Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 151 to 200 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
76 db83 protein. [swissprot;acc:p57088] Divided 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
77 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Divided 254.692 1.2567
Subtracted 52.024
78 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 254.691 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 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]
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 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] 294.053 242.562 51.491
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Divided 254.691 202.668 1.25669
81 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Subtracted 252.371 202.016 50.355
voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Divided 254.614 202.646 1.25645
82 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 267.636 335.359 1.25304
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Subtracted 252.329 202.004 50.325
83 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 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
84 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Subtracted 252.296 201.995 50.301
85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 88.2482 110.265 1.24949
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted 296.677 247.559 49.118
86 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 335 286 49
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Divided 88.2482 110.265 1.24949
87 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Subtracted 249.663 298.263 48.6
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Divided 88.2482 110.265 1.24949
88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Subtracted 249.663 298.263 48.6
89 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided 88.2482 110.265 1.24949
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Subtracted 249.663 298.263 48.6
90 necdin. [swissprot;acc:q99608] 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] Subtracted 249.663 298.263 48.6
91 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided 88.2482 110.265 1.24949
transcription factor lbx1. [swissprot;acc:p52954] Subtracted 249.663 298.263 48.6
92 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided 88.2482 110.265 1.24949
mosaic protein lgn. [swissprot;acc:p81274] Subtracted 249.663 298.263 48.6
93 melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided 88.2482 110.265 1.24949
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Subtracted 249.663 298.263 48.6
94 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Divided 88.2482 110.265 1.24949
95 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Subtracted 249.663 298.263 48.6
96 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 201.949 153.671 48.278
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Divided 88.2482 110.265 1.24949
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] Subtracted 271.752 225.68 46.072
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Divided 88.2482 110.265 1.24949
98 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Subtracted 204.641 160.957 43.684
99 jun dimerization protein. [refseq;acc:nm_130469]
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Divided 88.2482 110.265 1.24949
100 fos-related antigen 2. [swissprot;acc:p15408] Subtracted 204.641 161.046 43.595
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Divided 88.2482 110.265 1.24949

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/