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.


Navigation/Query Panel:
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 [...,...].
Hugo measured Gene expected Rank description final
Results: HTML CSV LaTeX Showing element 702 to 751 of 3206 in total
Hugo
measured
expected
Rank
description
final
C6orf130 0.0184372 0.333333 3176 0.055311655
C6orf153 0.0966625 0.421972 2081 0.229073256
C6orf32 0.0391646 0.152962 963 0.25604137
C7orf20 0.116413 0.536227 2444 0.217096491
C7orf24 0.0309189 0.138615 2254 0.223055946
C8orf53 0.0766245 0.327833 1837 0.233730283
C8orf79 0.0384193 0.138512 418 0.277371636
C9orf23 0.121488 0.616542 2812 0.197047403
C9orf41 0.557991 1.56247 125 0.357121097
C9orf68 0.138195 1 2987 0.138195
C9orf7 0.110103 0.445662 1263 0.247054943
C9orf95 0.0926874 0.515188 2889 0.179909858
CABC1 0.0340138 0.142333 1650 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" 0.238973393
CACNG2 0.0571433 0.587978 3095 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-2 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-2 SUBUNIT). [SWISSPROT;Acc:Q9Y698] 0.097186119
CACNG3 0.0570584 0.587107 3097 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-3 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-3 SUBUNIT). [SWISSPROT;Acc:O60359] 0.097185692
CACNG4 0.0573556 0.590154 3094 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-4 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-4 SUBUNIT). [SWISSPROT;Acc:Q9UBN1] 0.097187514
CACNG5 0.0760798 0.782104 3093 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-5 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-5 SUBUNIT). [SWISSPROT;Acc:Q9UF02] 0.09727581
CACNG8 0.0570584 0.587107 3096 VOLTAGE-DEPENDENT CALCIUM CHANNEL GAMMA-8 SUBUNIT (NEURONAL VOLTAGE- GATED CALCIUM CHANNEL GAMMA-8 SUBUNIT). [SWISSPROT;Acc:Q8WXS5] 0.097185692
CAD 0.341867 1.49271 2083 CAD PROTEIN [INCLUDES: GLUTAMINE-DEPENDENT CARBAMOYL-PHOSPHATE SYNTHASE (EC 6.3.5.5); ASPARTATE CARBAMOYLTRANSFERASE (EC 2.1.3.2); DIHYDROOROTASE (EC 3.5.2.3)]. [SWISSPROT;Acc:P27708] 0.229024392
CALR 0.205692 0.834998 1280 CALRETICULIN PRECURSOR (CRP55) (CALREGULIN) (HACBP) (ERP60). [SWISSPROT;Acc:P27797] 0.246338315
CAMK2A 0.141368 0.532171 681 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN (EC 2.7.1.123) (CAM-KINASE II ALPHA CHAIN) (CAM KINASE II ALPHA SUBUNIT) (CAMK-II ALPHA SUBUNIT). [SWISSPROT;Acc:Q9UQM7] 0.265643938
CAMK2B 0.159505 0.600447 682 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II BETA CHAIN (EC 2.7.1.123) (CAM-KINASE II BETA CHAIN) (CAM KINASE II BETA SUBUNIT) (CAMK-II BETA SUBUNIT). [SWISSPROT;Acc:Q13554] 0.265643762
CAMK2D 683 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN (EC 2.7.1.123) (CAM-KINASE II DELTA CHAIN) (CAM KINASE II DELTA SUBUNIT) (CAMK-II DELTA SUBUNIT). [SWISSPROT;Acc:Q13557]
CAMK2G 0.139426 0.524861 689 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN (EC 2.7.1.123) (CAM-KINASE II GAMMA CHAIN) (CAM KINASE II GAMMA SUBUNIT) (CAMK-II GAMMA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q13555] 0.265643666
CANT1 0.116337 0.580323 2783 CA2+-DEPENDENT ENDOPLASMIC RETICULUM NUCLEOSIDE DIPHOSPHATASE; APYRASE; SOLUBLE CALCIUM-ACTIVATED NUCLEOTIDASE SCAN-1. [RefSeq;Acc:NM_138793] 0.200469394
CANX 0.0429594 0.169952 1050 CALNEXIN PRECURSOR (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN-BINDING PROTEIN P88) (P90) (IP90). [SWISSPROT;Acc:P27824] 0.252773724
CAP1 0.136076 0.567058 1603 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 1 (CAP 1). [SWISSPROT;Acc:Q01518] 0.239968398
CAP2 0.132388 0.551914 1607 ADENYLYL CYCLASE-ASSOCIATED PROTEIN 2 (CAP 2). [SWISSPROT;Acc:P40123] 0.239870704
CAPN1 0.205623 0.685711 301 "CALPAIN 1, LARGE [CATALYTIC] SUBUNIT (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (MU-TYPE) (MUCANP) (MICROMOLAR-CALPAIN). [SWISSPROT;Acc:P07384]" 0.299868312
CAPN2 0.201663 0.672496 300 "CALPAIN 2, LARGE [CATALYTIC] SUBUNIT PRECURSOR (EC 3.4.22.17) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP) (M-TYPE) (M-CALPAIN) (MILLIMOLAR-CALPAIN) (CALPAIN LARGE POLYPEPTIDE L2). [SWISSPROT;Acc:P17655]" 0.299872416
CAPNS1 0.133134 0.368655 118 "CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT (CALPAIN REGULATORY SUBUNIT) (CALCIUM-ACTIVATED NEUTRAL PROTEINASE) (CANP). [SWISSPROT;Acc:P04632]" 0.361134394
CAPS 0.0480742 0.172225 380 CALCYPHOSINE. [SWISSPROT;Acc:Q13938] 0.279136014
CAPSL 0.0666911 0.23892 381 0.279135694
CAPZA1 0.12721 0.47397 621 F-ACTIN CAPPING PROTEIN ALPHA-1 SUBUNIT (CAPZ ALPHA-1). [SWISSPROT;Acc:P52907] 0.268392514
CAPZA3 0.0330141 0.124574 711 F-ACTIN CAPPING PROTEIN ALPHA-3 SUBUNIT (CAPZ ALPHA-3) (GERM CELL- SPECIFIC PROTEIN 3). [SWISSPROT;Acc:Q96KX2] 0.265015974
CAPZB 0.238765 0.900943 710 F-ACTIN CAPPING PROTEIN BETA SUBUNIT (CAPZ BETA). [SWISSPROT;Acc:P47756] 0.265016766
CASK 0.685788 2.77992 1269 PERIPHERAL PLASMA MEMBRANE PROTEIN CASK (EC 2.7.1.-) (HCASK) (CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE) (LIN-2 HOMOLOG). [SWISSPROT;Acc:O14936] 0.24669343
CASP3 0.0223509 0.0954818 1829 APOPAIN PRECURSOR (EC 3.4.22.-) (CYSTEINE PROTEASE CPP32) (YAMA PROTEIN) (CPP-32) (CASPASE-3) (CASP-3) (SREBP CLEAVAGE ACTIVITY 1) (SCA-1). [SWISSPROT;Acc:P42574] 0.234085449
CASP7 0.028203 0.120482 1830 CASPASE-7 PRECURSOR (EC 3.4.22.-) (ICE-LIKE APOPTOTIC PROTEASE 3) (ICE-LAP3) (APOPTOTIC PROTEASE MCH-3) (CMH-1). [SWISSPROT;Acc:P55210] 0.23408476
CBL 0.394562 1.04353 94 CBL E3 UBIQUITIN PROTEIN LIGASE (EC 6.3.2.-) (SIGNAL TRANSDUCTION PROTEIN CBL) (PROTO-ONCOGENE C-CBL). [SWISSPROT;Acc:P22681] 0.378103169
CBLB 0.502064 1.32571 93 SIGNAL TRANSDUCTION PROTEIN CBL-B (SH3-BINDING PROTEIN CBL-B). [SWISSPROT;Acc:Q13191] 0.378713293
CBS 0.262879 1.25182 2637 CYSTATHIONINE BETA-SYNTHASE (EC 4.2.1.22) (SERINE SULFHYDRASE) (BETA-THIONASE). [SWISSPROT;Acc:P35520] 0.209997444
CBX1 0.185372 1.18579 2939 CHROMOBOX PROTEIN HOMOLOG 1 (HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA) (HP1 BETA) (MODIFIER 1 PROTEIN) (M31) (HETEROCHROMATIN PROTEIN P25). [SWISSPROT;Acc:P23197] 0.156327849
CBX3 0.158961 1.02341 2940 CHROMOBOX PROTEIN HOMOLOG 3 (HETEROCHROMATIN PROTEIN 1 HOMOLOG GAMMA) (HP1 GAMMA) (MODIFIER 2 PROTEIN) (HECH). [SWISSPROT;Acc:Q13185] 0.155324845
CBX5 0.15563 1.00293 2941 CHROMOBOX PROTEIN HOMOLOG 5 (HETEROCHROMATIN PROTEIN 1 HOMOLOG ALPHA) (HP1 ALPHA) (ANTIGEN P25). [SWISSPROT;Acc:P45973] 0.155175336
CC2D1A 0.0886161 1.29368 3129 0.068499242
CCBL1 0.113234 0.550484 2727 CYTOPLASMIC CYSTEINE CONJUGATE-BETA LYASE; GLUTAMINE-PHENYLPYRUVATE AMINOTRANSFERASE. [RefSeq;Acc:NM_004059] 0.205698985
CCBL2 0.087666 0.42621 2730 0.205687337
CCDC104 0.0476371 1.01816 3185 0.04678744
CCDC12 0.0389719 0.139616 377 0.279136345

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/