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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 608 to 657 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
152 SEPT8 Squared septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 90226 126939 1.4069
153 no value ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 70011 49783 1.40632
LUC7L Rooted luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 55.297 65.9236 1.19217
MAGEE2 Measured hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 23693.7 18263 1.29736
RBM15B Ranked chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] 249.663 298.263 1.19466
154 no value Measured melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 23693.7 18263 1.29736
CCT3 Squared t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] 42788.3 60162.6 1.40605
EIF5 Rooted eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 43.5479 51.5473 1.18369
RGS19 Ranked regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] 249.663 298.263 1.19466
155 CSTF2 Squared cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] 126408 89940.5 1.40546
MAGEA11 Measured melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 23693.7 18263 1.29736
RBM15 Ranked putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 249.663 298.263 1.19466
SNRPD2 Rooted small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 55.7423 65.6839 1.17835
156 MAGEA2B Measured melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 23693.7 18263 1.29736
RGS20 Ranked 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] 249.663 298.263 1.19466
SEPT10 Squared septin 10 isoform 1. [refseq;acc:nm_144710] 89578.7 125883 1.40528
SH2D3C Rooted sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 56.3447 66.124 1.17356
157 no value Measured hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 23693.7 18263 1.29736
BRP44 Squared brain protein 44. [swissprot;acc:o95563] 89182.8 125229 1.40418
EIF4G3 Rooted eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 52.7582 61.9123 1.17351
LBX1 Ranked transcription factor lbx1. [swissprot;acc:p52954] 249.663 298.263 1.19466
158 BCAR3 Rooted breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 56.3507 66.1252 1.17346
GPSM2 Ranked mosaic protein lgn. [swissprot;acc:p81274] 249.663 298.263 1.19466
MAGEA6 Measured melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 23693.7 18263 1.29736
SEPT7 Squared septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 89182.8 125229 1.40418
159 no value Rooted rna-binding protein. [refseq;acc:nm_019027] 52.7642 61.9019 1.17318
NDN Measured necdin. [swissprot;acc:q99608] 23693.7 18263 1.29736
RGS17 Ranked regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 249.663 298.263 1.19466
SEPT6 Squared septin 6. [swissprot;acc:q14141] 88953.6 124854 1.40359
160 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 173408 242989 1.40126
Rooted apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 52.7642 61.9019 1.17318
GNAO1 Ranked guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 249.663 298.263 1.19466
MAGED1 Measured melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 23693.7 18263 1.29736
161 HOXB4 Squared homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 173408 242989 1.40126
MAGEF1 Measured melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 23693.7 18263 1.29736
RAP1GAP Ranked rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 249.663 298.263 1.19466
SYNCRIP Rooted ns1-associated protein 1. [refseq;acc:nm_006372] 52.7642 61.9019 1.17318
162 HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
HOXC5 Squared homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 173408 242989 1.40126
MAGEB6B Measured melanoma antigen, family b, 6. [refseq;acc:nm_173523] 23693.7 18263 1.29736
NOSTRIN Ranked nostrin. [refseq;acc:nm_052946] 209.299 249.187 1.19058
163 no value Measured melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 23693.7 18263 1.29736
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 173408 242989 1.40126
EIF4G1 Rooted eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 52.7702 61.8915 1.17285
SNF8 Ranked eap30 subunit of ell complex. [refseq;acc:nm_007241] 209.299 249.187 1.19058
164 HOXD4 Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 173408 242989 1.40126
MAGEA9 Measured melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 23693.7 18263 1.29736
MXD1 Rooted mad protein (max dimerizer). [swissprot;acc:q05195] 55.646 65.1534 1.17086
SLC39A6 Ranked liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 209.299 249.187 1.19058
165 GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]

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
- Hugo is the HGNC identifier if it exists
- 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/