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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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 [...,...].
Rank Gene Hugo Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1880 to 1929 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
Network Comparison Type
description
Interaction Map
red
green
network_comparison
470 TMOD1 Subtracted tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Low confidence 209.136 202.478 6.658
471 LAMC1 Divided laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 248.152 267.226 1.07686
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Low confidence 208.29 201.499 1.0337
SNX9 Subtracted sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] 209.136 202.478 6.658
ZNF622 zinc finger-like protein 9. [refseq;acc:nm_033414] High confidence 250.942 235.004 15.938
472 PLRG1 Divided pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Low confidence 201.847 195.283 1.03361
SLC45A2 Subtracted membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] High confidence 250.942 235.004 15.938
SLC46A2 Divided thymic stromal co-transporter. [refseq;acc:nm_033051] 248.152 267.226 1.07686
TMOD2 Subtracted neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Low confidence 209.136 202.478 6.658
473 no value guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] High confidence 250.942 235.004 15.938
EXOC1 Divided exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Low confidence 209.111 202.34 1.03346
PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 225.661 209.651 1.07637
TNK2 Subtracted activated p21cdc42hs kinase. [refseq;acc:nm_005781] Low confidence 209.136 202.478 6.658
474 KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] High confidence 226.727 210.816 15.911
KCNA2 Divided potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 226.789 210.818 1.07576
PRPF40B Subtracted huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 201.429 194.776 6.653
RRAGB Divided ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 171.213 165.68 1.0334
475 FUCA2 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] 202.311 195.778 1.03337
KCNA1 potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] High confidence 226.727 210.816 1.07547
MEMO1P Subtracted protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] 236.964 252.86 15.896
SLC7A5 large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] Low confidence 201.466 194.819 6.647
476 FUCA1 Divided tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] 202.271 195.742 1.03336
KCNA4 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] High confidence 226.681 210.814 1.07527
Subtracted 15.867
PRRX1 paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821] Low confidence 194.41 201.036 6.626
477 ARHGEF7 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] High confidence 220.183 236.015 15.832
HNRNPR Divided heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Low confidence 203.823 197.249 1.03333
NIP7 saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101] High confidence 251.926 234.547 1.0741
SAMSN1 Subtracted sam-domain protein samsn-1 (sam domain, sh3 domain and nuclear localisation signals protein 1). [swissprot;acc:q9nsi8] Low confidence 204.278 210.893 6.615
478 BLVRB Divided flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [swissprot;acc:p30043] 207.68 214.591 1.03328
BRF1 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] High confidence 228.051 212.321 1.07409
PAK2 Subtracted serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] 220.171 235.979 15.808
SASH1 sam and sh3 domain containing 1. [refseq;acc:nm_015278] Low confidence 204.276 210.886 6.61
479 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 194.137 187.552 6.585
COG5 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 235.98 15.808
NOLA1 Divided nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 228.051 212.321 1.07409
VTA1 protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] Low confidence 207.68 214.591 1.03328
480 C15orf15 Subtracted ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 206.763 200.18 6.583
NETO2 Divided neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] High confidence 237.109 254.667 1.07405
PAK1 Subtracted serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] 220.172 235.98 15.808
SYNCRIP Divided ns1-associated protein 1. [refseq;acc:nm_006372] Low confidence 203.822 197.259 1.03327
481 HNRNPR Subtracted heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 203.823 197.249 6.574
NETO1 Divided neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] High confidence 237.109 254.667 1.07405
PAK3 Subtracted serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 220.171 235.979 15.808
RRAGA Divided ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 171.564 166.045 1.03324
482 ARHGEF6 Subtracted rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] High confidence 220.161 235.95 15.789
HNRNPU Divided heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] 237.109 254.667 1.07405
PLRG1 Subtracted pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Low confidence 201.847 195.283 6.564
TRIP12 Divided thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 204.65 198.086 1.03314
483 no value rna-binding protein. [refseq;acc:nm_019027] 203.821 197.289 1.03311

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/