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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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description Gene Rank measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2558 to 2607 of 3206 in total
description
Rank
measured
expected
final
Hugo
RAL-A EXCHANGE FACTOR RALGPS2. [RefSeq;Acc:NM_152663] 920 0.040067 0.155337 0.257935971 RALGPS2
RAN BINDING PROTEIN 11. [RefSeq;Acc:NM_016338] 1802 0.0547985 0.233549 0.234633846 IPO11
RAN-BINDING PROTEIN 2 (RANBP2) (NUCLEAR PORE COMPLEX PROTEIN NUP358) (NUCLEOPORIN NUP358) (358 KDA NUCLEOPORIN) (P270). [SWISSPROT;Acc:P49792] 646 0.464913 1.73399 0.268117463 RANBP2
RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 647 0.39546 1.47537 0.268041237 no value
648 0.365822 1.365 0.268001465
RAN-GTP BINDING PROTEIN (FRAGMENT). [SPTREMBL;Acc:O60518] 237 0.151819 0.482771 0.31447415 RANBP6
RAP1 GTPASE-ACTIVATING PROTEIN 1 (RAP1GAP). [SWISSPROT;Acc:P47736] 2934 0.018683 0.117937 0.158415086 RAP1GAP
RAS GTPASE-ACTIVATING PROTEIN NGAP (RAS PROTEIN ACTIVATOR LIKE 1). [SWISSPROT;Acc:Q9UJF2] 3073 0.0550688 0.533628 0.103196984 RASAL2
RAS SUPPRESSOR PROTEIN 1 (RSU-1) (RSP-1). [SWISSPROT;Acc:Q15404] 2508 0.214312 0.997879 0.214767522 RSU1
RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 1 (GAP SH3-DOMAIN BINDING PROTEIN 1) (G3BP-1). [SWISSPROT;Acc:Q13283] 2519 0.0506049 0.235627 0.214766983 G3BP1
RAS-GTPASE-ACTIVATING PROTEIN BINDING PROTEIN 2 (GAP SH3-DOMAIN BINDING PROTEIN 2) (G3BP-2). [SWISSPROT;Acc:Q9UN86] 2518 0.0598238 0.278552 0.214767081 G3BP2
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 (P21-RAC1) (RAS-LIKE PROTEIN TC25). [SWISSPROT;Acc:P15154] 1475 0.0733796 0.302004 0.24297559 no value
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 (P21-RAC2) (SMALL G PROTEIN) (GX). [SWISSPROT;Acc:P15153] 1479 0.0532303 0.219077 0.242975301 RAC2
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 (P21-RAC3). [SWISSPROT;Acc:O14658] 1474 0.0569548 0.234405 0.242976046 RAC3
RAS-RELATED GTP BINDING A; RAS-RELATED GTP-BINDING PROTEIN. [RefSeq;Acc:NM_006570] 3200 0.0391808 1.63989 0.023892334 RRAGA
RAS-RELATED GTP BINDING B SHORT ISOFORM; GTP-BINDING PROTEIN RAGB. [RefSeq;Acc:NM_006064] 3203 0.0426192 1.78381 0.023892231 RRAGB
RAS-RELATED GTP BINDING C; RAG C PROTEIN. [RefSeq;Acc:NM_022157] 3201 0.029 1.21378 0.023892303 RRAGC
RAS-RELATED PROTEIN RAB-26. [SWISSPROT;Acc:Q9ULW5] 2067 0.016721 0.0728736 0.229452092 RAB26
RAS-RELATED PROTEIN RAB-37. [SWISSPROT;Acc:Q96AX2] 2068 0.0208556 0.0908932 0.229451708 RAB37
RD PROTEIN. [SWISSPROT;Acc:P18615] 213 0.155654 0.485577 0.320554721 no value
RECEPTOR PROTEIN-TYROSINE KINASE ERBB-2 PRECURSOR (EC 2.7.1.112) (P185ERBB2) (NEU PROTO-ONCOGENE) (C-ERBB-2) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2) (MLN 19). [SWISSPROT;Acc:P04626] 1493 0.0803487 0.330932 0.242795197 ERBB2
RECEPTOR PROTEIN-TYROSINE KINASE ERBB-3 PRECURSOR (EC 2.7.1.112) (C-ERBB3) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER3). [SWISSPROT;Acc:P21860] 1489 0.0992034 0.408587 0.242796271 ERBB3
RECEPTOR PROTEIN-TYROSINE KINASE ERBB-4 PRECURSOR (EC 2.7.1.112) (P180ERBB4) (TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER4). [SWISSPROT;Acc:Q15303] 1490 ERBB4
REGUCALCIN GENE PROMOTOR REGION RELATED PROTEIN; RGPR-P117. [RefSeq;Acc:NM_033127] 447 0.109365 0.395349 0.276629004 SEC16B
REGULATOR OF CHROMOSOME CONDENSATION (CELL CYCLE REGULATORY PROTEIN). [SWISSPROT;Acc:P18754] 2455 0.118612 0.5473 0.21672209 RCC1
REGULATOR OF G-PROTEIN SIGNALING 17 (RGS17). [SWISSPROT;Acc:Q9UGC6] 2930 0.0147736 0.0932586 0.158415417 RGS17
REGULATOR OF G-PROTEIN SIGNALING 19 (RGS19) (G-ALPHA INTERACTING PROTEIN) (GAIP PROTEIN). [SWISSPROT;Acc:P49795] 2932 0.0145774 0.0920202 0.158415218 RGS19
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] 2933 0.018683 0.117937 0.158415086 RGS20
REPLICATION PROTEIN A 32 KDA SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 2). [SWISSPROT;Acc:P15927] 1057 0.160828 0.636513 0.252670409 RPA2
REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT (RP-A) (RF-A) (REPLICATION FACTOR-A PROTEIN 1) (SINGLE-STRANDED DNA-BINDING PROTEIN). [SWISSPROT;Acc:P27694] 1056 0.0688366 0.272436 0.252670719 RPA1
REPRESSOR OF ESTROGEN RECEPTOR ACTIVITY; B-CELL ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007273] 2404 0.26817 1.22481 0.218948245 no value
REST COREPRESSOR. [RefSeq;Acc:NM_015156] 709 0.0422874 0.159487 0.265146376 RCOR1
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] 2878 0.101998 0.546053 0.186791392 no value
RETICULON 1 (NEUROENDOCRINE-SPECIFIC PROTEIN). [SWISSPROT;Acc:Q16799] 2691 0.268811 1.29069 0.20826922 RTN1
RETICULON 4 (NEURITE OUTGROWTH INHIBITOR) (NOGO PROTEIN) (FOOCEN) (NEUROENDOCRINE-SPECIFIC PROTEIN) (NSP) (NEUROENDOCRINE SPECIFIC PROTEIN C HOMOLOG) (RTN-X) (RETICULON 5) (MY043 PROTEIN). [SWISSPROT;Acc:Q9NQC3] 2692 0.267978 1.28698 0.20822235 RTN4
RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] 2685 0.175589 0.842838 0.208330664 RTN2
RETICULON PROTEIN 3 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 2) (NSP-LIKE PROTEIN II) (NSPLII). [SWISSPROT;Acc:O95197] 2683 0.203468 0.976589 0.208345578 RTN3
RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN 65KDA; RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN (65KD); RETINITIS PIGMENTOSA 20 (AUTOSOMAL RECESSIVE). [RefSeq;Acc:NM_000329] 281 0.0427222 0.141553 0.301810629 RPE65
RETINAL SHORT-CHAIN DEHYDROGENASE/REDUCTASE 3. [RefSeq;Acc:NM_016246] 2977 0.518329 3.71404 0.139559348 HSD17B14
RETINOBLASTOMA-LIKE PROTEIN 1 (107 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB1) (P107). [SWISSPROT;Acc:P28749] 1038 0.128252 0.506251 0.253336784 RBL1
RETINOBLASTOMA-LIKE PROTEIN 2 (130 KDA RETINOBLASTOMA-ASSOCIATED PROTEIN) (PRB2) (P130) (RBR-2). [SWISSPROT;Acc:Q08999] 1030 0.152107 0.600397 0.253344037 RBL2
RETINOIC ACID INDUCED 17; PIAS-LIKE PROTEIN HZIMP10. [RefSeq;Acc:NM_020338] 649 0.204901 0.765015 0.267839193 ZMIZ1
RETINOL DEHYDROGENASE 8 (ALL-TRANS); PHOTORECEPTOR OUTER SEGMENT ALL-TRANS RETINOL DEHYDROGENASE. [RefSeq;Acc:NM_015725] 1779 0.0319409 0.135713 0.23535623 RDH8
REV1-LIKE; REV1 PROTEIN; REV1 (YEAST HOMOLOG)- LIKE. [RefSeq;Acc:NM_016316] 177 0.120377 0.356839 0.337342611 REV1
RGS19-INTERACTING PROTEIN 1 (GAIP C-TERMINUS INTERACTING PROTEIN GIPC) (RGS-GAIP INTERACTING PROTEIN) (TAX INTERACTION PROTEIN 2) (TIP-2). [SWISSPROT;Acc:O14908] 86 1.20591 3.1266 0.385693725 GIPC1
RH TYPE C GLYCOPROTEIN. [RefSeq;Acc:NM_016321] 2585 0.077662 0.364414 0.213114754 RHCG
RHESUS BLOOD GROUP-ASSOCIATED GLYCOPROTEIN (ERYTHROCYTE PLASMA MEMBRANE 50 KDA GLYCOPROTEIN) (RH50A). [SWISSPROT;Acc:Q02094] 2583 0.062927 0.295267 0.213118974 RHAG
RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 ISOFORM A; APC-STIMULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR. [RefSeq;Acc:NM_015320] 2091 0.0362539 0.158511 0.228715357 ARHGEF4
RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 6 (PAK-INTERACTING EXCHANGE FACTOR ALPHA) (ALPHA-PIX) (COOL-2). [SWISSPROT;Acc:Q15052] 2181 0.257131 1.13453 0.226640988 ARHGEF6
RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 (PAK-INTERACTING EXCHANGE FACTOR BETA) (BETA-PIX) (COOL-1) (P85). [SWISSPROT;Acc:Q14155] 2186 0.214133 0.945656 0.226438578 ARHGEF7

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/