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 358 to 407 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
90 necdin. [swissprot;acc:q99608] Ranked 88.2482 110.265 1.24949
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Measured 2414.77 1698.75 1.4215
transforming protein n-ras. [swissprot;acc:p01111] Squared 105469 64130.2 1.64461
91 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 37.3005 48.4141 1.29795
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked 88.2482 110.265 1.24949
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Measured 2416.53 1700.8 1.42082
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 1.60615
92 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Measured 4117.67 5801.04 1.40882
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 88.2482 110.265 1.24949
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Squared 29570.7 18601.8 1.58967
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Rooted 37.3005 48.4141 1.29795
93 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Squared 29567 18601.6 1.58949
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted 37.3005 48.4141 1.29795
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Measured 4245.52 5942.75 1.39977
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Ranked 88.2482 110.265 1.24949
94 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted 47.6504 36.9304 1.29028
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 4247.86 5941.88 1.39879
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Ranked 88.2482 110.265 1.24949
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared 84857.8 53402.4 1.58903
95 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Ranked 88.2482 110.265 1.24949
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Squared 256169 162517 1.57626
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Rooted 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
96 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Squared 7744.68 4959.41 1.56161
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured 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
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 2820.51 3897.1 1.3817
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 227160 146079 1.55505
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Ranked 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
98 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Ranked 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
transcription factor lbx1. [swissprot;acc:p52954] Rooted 47.6504 36.9304 1.29028
trs85 homolog. [swissprot;acc:q9y2l5] Squared 227160 146079 1.55505
99 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Ranked 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
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Squared 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
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Ranked 88.2482 110.265 1.24949
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Rooted 47.6504 36.9304 1.29028
101 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Squared 222655 143584 1.5507
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Measured 2353.63 3225.65 1.3705
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Rooted 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
102 fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Squared 214143 138337 1.54798
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] Ranked 88.2482 110.265 1.24949
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 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/