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 700 to 749 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
88 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 1 2411.93 1695.45 1.42259
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 48.4141 1.29795
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared 105482 64137.2 1.64463
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Measured 0 304.664 483.809 1.58801
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Squared 13.9318 32.9409 2.36444
89 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Measured 1 2414.22 1698.12 1.4217
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Rooted 0 39.9124 52.9528 1.32673
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Squared 21.5282 9.12314 2.35974
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Ranked 1 88.2482 110.265 1.24949
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 0 5677.58 4549.85 1.24786
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] Rooted 1 37.3005 48.4141 1.29795
suppressor of actin 1. [refseq;acc:nm_014016] Measured 0 23.6076 37.4843 1.58781
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 1 105473 64132.3 1.64462
90 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 67.8804 159.002 2.34238
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] Rooted 1 37.3005 48.4141 1.29795
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Ranked 0 5677.45 4550.87 1.24755
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] Rooted 24.6374 32.6803 1.32645
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Measured 34.6667 54.6667 1.57692
necdin. [swissprot;acc:q99608] Ranked 1 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 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Ranked 0 13841.2 11127.5 1.24387
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 1 37.3005 48.4141 1.29795
lats homolog 1. [refseq;acc:nm_004690] Squared 0 12.5892 5.42219 2.32179
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Ranked 1 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
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 0 39.7924 62.2106 1.56338
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 1 90432.9 56304.2 1.60615
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Rooted 0 11.5003 8.68906 1.32354
92 adp-ribosylation factor 3. [swissprot;acc:p16587] Measured 300.697 469.346 1.56086
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 1 4117.67 5801.04 1.40882
dok-like protein. [refseq;acc:nm_024872] Ranked 0 17571 21783 1.23971
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Rooted 25.1701 33.2721 1.32189
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Ranked 1 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
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Squared 0 12.5892 5.42219 2.32179
93 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 1 29567 18601.6 1.58949
cab2. [refseq;acc:nm_033419] Rooted 0 0.00001 13.1909 1319090
cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1 37.3005 48.4141 1.29795
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Measured 0 528.5 816.5 1.54494
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 1 4245.52 5942.75 1.39977
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Ranked 88.2482 110.265 1.24949
myosin vi. [swissprot;acc:q9um54] Squared 0 39.56 17.2035 2.29953
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Ranked 7739.47 9580.95 1.23793
94 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Squared 122.543 53.9854 2.26993
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] Rooted 1 47.6504 36.9304 1.29028
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] 0 24.7769 18.7862 1.31889
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Measured 1 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

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/