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 description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 1362 to 1411 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
network_comparison
green
171 LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted Divided 61.6639 1.16333 71.7355
MAGED2 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] Measured 23693.7 1.29736 18263
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Subtracted 4117.67 1683.37 5801.04
SNAI2 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Squared 69165 16173.3 52991.7
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 11.1171 66.7332
TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Ranked Divided 227.202 1.17829 192.823
TRPC4 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Subtracted 201.478 27.306 228.784
172 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted 55.6161 11.1171 66.7332
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Measured 4556.78 1611.52 2945.26
CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Squared Divided 121579 1.39331 87259.3
CTBP1 c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] Subtracted 69123.3 16156.3 52967
SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted Divided 56.7592 1.16261 65.9889
TBC1D10A ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Ranked Subtracted 201.515 27.237 228.752
TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 174.667 1.17685 205.556
TRO trophinin. [swissprot;acc:q12816] Measured 23693.7 1.29736 18263
173 no value methyltransferase like 2. [refseq;acc:nm_018396] Squared Subtracted 71576.8 15250.1 56326.7
BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Measured Divided 4579.34 1.29727 5940.64
MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted 145.551 1.1597 168.796
PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured Subtracted 4556.79 1611.51 2945.28
PSEN2 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 11.1136 48.4141
SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Squared Divided 82624.3 1.39258 115061
SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Ranked 227.032 1.17599 193.056
TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Subtracted 201.515 27.237 228.752
174 DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Divided 335 1.17133 286
DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared Subtracted 71576.8 15250.1 56326.7
LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Ranked 228.1 27.132 200.968
MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] Measured Divided 4455.95 1.2958 5774.03
PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 1.1597 168.796
PPP2R2B serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Measured Subtracted 4556.83 1611.45 2945.38
SKP1A 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 37.3005 11.1136 48.4141
ZNF547 sedlin. [swissprot;acc:o14582] Squared Divided 112820 1.39189 157033
175 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked 199.949 1.17123 234.187
FBXW7 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 Subtracted 37.3005 11.1136 48.4141
FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 15250.1 56326.7
LUC7L luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 228.085 27.079 201.006
MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured Divided 4456.67 1.29553 5773.77
PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Rooted 145.551 1.1597 168.796
PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured Subtracted 4556.99 1611.19 2945.8
176 CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted 37.3005 11.1136 48.4141
EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 26.849 244.167
HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured 10235.2 1595.6 11830.8
MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 4456.93 1.29544 5773.67
PANK3 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Rooted 145.551 1.1597 168.796
PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Squared Subtracted 71576.8 15250.1 56326.7
POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked Divided 275.754 1.1689 235.908
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Squared 112820 1.39189 157033
177 ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Subtracted 9924.76 15221.8 25146.6
LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured 4110.14 1584.85 5694.99
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked Divided 229.406 1.1663 196.695

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/