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 1773 to 1822 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
444 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 0 14556.7 14237.8 1.0224
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 1 223.801 207.549 1.0783
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Subtracted 250.053 233.725 16.328
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 0 11290.8 11525.8 235
445 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 10028.5 10261.5 233
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Divided 7965.06 7790.78 1.02237
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 1 223.801 207.549 1.0783
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Subtracted 250.858 234.563 16.295
446 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 0 9897.12 9690.83 206.29
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided 7965.06 7790.78 1.02237
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 1 224.049 207.785 1.07827
Subtracted 16.264
447 protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 0 12532.2 12808.8 1.02207
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Subtracted 9141.6 8940.14 201.46
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Divided 1 224.049 207.785 1.07827
Subtracted 16.264
448 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 16.252
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] 0 8770.94 8574.04 196.9
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] Divided 1 228.468 246.338 1.07822
protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] 0 2939 2876 1.02191
449 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] 9897.12 9690.83 1.02129
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 1 228.463 246.33 1.07821
histone h2b.d (h2b/d). [swissprot;acc:q99877] Subtracted 0 8770.82 8574.19 196.63
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 1 223.801 207.549 16.252
450 histone h2b.s (h2b/s). [swissprot;acc:p57053] 0 8770.41 8574.66 195.75
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 1 223.801 207.549 16.252
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 235.94 218.837 1.07815
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 0 11290.8 11525.8 1.02081
451 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 14010.2 13737.2 1.01987
histone h2b. [refseq;acc:nm_175055] Subtracted 8770.3 8574.79 195.51
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 1 223.79 207.539 16.251
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Divided 239.092 257.705 1.07785
452 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
histone h2b.e (h2b/e). [swissprot;acc:q99879] Subtracted 0 8770.28 8574.81 195.47
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Divided 14010.2 13737.2 1.01987
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Subtracted 1 221.522 205.286 16.236
453 histone h2b.c (h2b/c). [swissprot;acc:q99880] 0 8770.14 8574.98 195.16
paxillin. [swissprot;acc:p49023] 1 221.522 205.286 16.236
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Divided 0 14010.2 13737.2 1.01987
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 1 224.161 207.972 1.07784
454 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 223.457 207.222 16.235
lats homolog 1. [refseq;acc:nm_004690] Divided 0 13933.5 14204.8 1.01947
scratch; scratch 1. [refseq;acc:nm_031309] Subtracted 12164.9 12358.1 193.2
455 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 1 224.161 207.972 16.189
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 0 12189.6 12378.3 188.7
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided 1 210.225 226.578 1.07779
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] 0 13933.5 14204.8 1.01947
456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 1 210.225 226.578 1.07779
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Subtracted 0 7965.06 7790.78 174.28

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/